Package: a4 Version: 1.6.1 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo License: GPL-3 Title: Automated Affymetrix Array Analysis Umbrella Package Description: Automated Affymetrix Array Analysis Umbrella Package biocViews: Bioinformatics, Microarray Author: Willem Talloen, Tobias Verbeke Maintainer: Tobias Verbeke MD5sum: 07bc5cbc782e672d63d5e6b6c87adf8c source.ver: src/contrib/a4_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4_1.6.1.zip win64.binary.ver: bin/windows64/contrib/2.15/a4_1.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4_1.6.1.tgz vignettes: vignettes/a4/inst/doc/a4vignette.pdf vignetteTitles: a4vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/a4/inst/doc/a4vignette.R Package: a4Base Version: 1.6.0 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL Enhances: gridSVG, JavaGD License: GPL-3 Title: Automated Affymetrix Array Analysis Base Package Description: Automated Affymetrix Array Analysis biocViews: Bioinformatics, Microarray Author: Willem Talloen, Tobias Verbeke, Tine Casneuf, An De Bondt, Steven Osselaer and Hinrich Goehlmann Maintainer: Tobias Verbeke MD5sum: 06406dfd887d97c639c179295f6b5b24 source.ver: src/contrib/a4Base_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Base_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Base_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Base_1.6.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4 Package: a4Classif Version: 1.6.0 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL License: GPL-3 Title: Automated Affymetrix Array Analysis Classification Package Description: Automated Affymetrix Array Analysis Classification Package biocViews: Bioinformatics, Microarray Author: Willem Talloen, Tobias Verbeke Maintainer: Tobias Verbeke MD5sum: a79af61ae6d5c88e352fab9fbb8fa33a source.ver: src/contrib/a4Classif_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Classif_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Classif_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Classif_1.6.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4 Package: a4Core Version: 1.6.0 Depends: methods, Biobase, glmnet License: GPL-3 Title: Automated Affymetrix Array Analysis Core Package Description: Automated Affymetrix Array Analysis Core Package biocViews: Bioinformatics, Microarray Author: Willem Talloen, Tobias Verbeke Maintainer: Tobias Verbeke MD5sum: 7b6a3c7b7cddb14f5b2bc0b1781e0379 source.ver: src/contrib/a4Core_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Core_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Core_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Core_1.6.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4, a4Base, a4Classif importsMe: a4Classif Package: a4Preproc Version: 1.6.0 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 Title: Automated Affymetrix Array Analysis Preprocessing Package Description: Automated Affymetrix Array Analysis Preprocessing Package biocViews: Bioinformatics, Microarray Author: Willem Talloen, Tobias Verbeke Maintainer: Tobias Verbeke MD5sum: d90391402175f298d1fe89f56c2e91bc source.ver: src/contrib/a4Preproc_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Preproc_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Preproc_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Preproc_1.6.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4, a4Base, a4Classif Package: a4Reporting Version: 1.6.0 Depends: methods, annaffy Imports: xtable, utils License: GPL-3 Title: Automated Affymetrix Array Analysis Reporting Package Description: Automated Affymetrix Array Analysis Reporting Package biocViews: Microarray Author: Tobias Verbeke Maintainer: Tobias Verbeke MD5sum: 3c5d221e8f5738788ab8adf0ccffa694 source.ver: src/contrib/a4Reporting_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Reporting_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Reporting_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Reporting_1.6.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4 Package: ABarray Version: 1.26.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL Title: Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data. Description: Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used. biocViews: Microarray, OneChannel, Preprocessing Author: Yongming Andrew Sun Maintainer: Yongming Andrew Sun MD5sum: 71c16f7a44ebb75bdbbdcc56655da985 source.ver: src/contrib/ABarray_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ABarray_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ABarray_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ABarray_1.26.0.tgz vignettes: vignettes/ABarray/inst/doc/ABarrayGUI.pdf, vignettes/ABarray/inst/doc/ABarray.pdf vignetteTitles: ABarray gene expression GUI interface, ABarray gene expression hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ABarray/inst/doc/ABarrayGUI.R, vignettes/ABarray/inst/doc/ABarray.R Package: aCGH Version: 1.36.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, cluster, grDevices, graphics, methods, multtest, stats, survival, splines, utils License: GPL-2 Archs: i386, x64 Title: Classes and functions for Array Comparative Genomic Hybridization data. Description: Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. biocViews: CopyNumberVariants, DataImport, Genetics Author: Jane Fridlyand , Peter Dimitrov Maintainer: Peter Dimitrov MD5sum: 77356c94eb4f384880cd4e4910ac12b6 source.ver: src/contrib/aCGH_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/aCGH_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/aCGH_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/aCGH_1.36.0.tgz vignettes: vignettes/aCGH/inst/doc/aCGH.pdf vignetteTitles: aCGH Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/aCGH/inst/doc/aCGH.R dependsOnMe: ADaCGH2, CRImage importsMe: snapCGH suggestsMe: beadarraySNP Package: ACME Version: 2.14.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods Imports: graphics, stats License: GPL (>= 2) Archs: i386, x64 Title: Algorithms for Calculating Microarray Enrichment (ACME) Description: ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. biocViews: Bioinformatics Author: Sean Davis Maintainer: Sean Davis URL: http://watson.nci.nih.gov/~sdavis MD5sum: 0643c42174550c40469b27560a54e8ff source.ver: src/contrib/ACME_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ACME_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ACME_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ACME_2.14.0.tgz vignettes: vignettes/ACME/inst/doc/ACME.pdf vignetteTitles: ACME hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ACME/inst/doc/ACME.R Package: ADaCGH2 Version: 1.8.0 Depends: R (>= 2.11.0), tilingArray, aCGH, waveslim, cluster, snapCGH, snowfall, ff Suggests: GLAD, DNAcopy, CGHregions, rlecuyer Enhances: Rmpi, multicore License: GPL (>= 3) Archs: i386, x64 Title: Analysis of data from aCGH experiments using parallel computing and ff objects Description: Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized. biocViews: Microarray, CopyNumberVariants Author: Ramon Diaz-Uriarte , Oscar M. Rueda . Wavelet-based aCGH smoothing code from Li Hsu and Douglas Grove . Imagemap code from Barry Rowlingson . HaarSeg code from Erez Ben-Yaacov; downloaded from Maintainer: Ramon Diaz-Uriarte URL: http://launchpad.net/adacgh, http://wavicgh.bioinfo.cnio.es MD5sum: eb2fb42169ef7626aa6d0dceccde0b23 source.ver: src/contrib/ADaCGH2_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ADaCGH2_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ADaCGH2_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ADaCGH2_1.8.0.tgz vignettes: vignettes/ADaCGH2/inst/doc/ADaCGH2.pdf vignetteTitles: ADaCGH2 Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ADaCGH2/inst/doc/ADaCGH2.R Package: adSplit Version: 1.28.0 Depends: R (>= 2.1.0), methods (>= 2.1.0) Imports: AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db (>= 1.8.1), graphics, grDevices, KEGG.db (>= 1.8.1), methods, multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) Archs: i386, x64 Title: Annotation-Driven Clustering Description: This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined. biocViews: Microarray, Bioinformatics, Clustering Author: Claudio Lottaz, Joern Toedling Maintainer: Claudio Lottaz URL: http://compdiag.molgen.mpg.de/software/index.shtml MD5sum: 0751ef28d4531c8a8c4abc7aeefb49c7 source.ver: src/contrib/adSplit_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/adSplit_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/adSplit_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/adSplit_1.28.0.tgz vignettes: vignettes/adSplit/inst/doc/bcb_logo.pdf, vignettes/adSplit/inst/doc/minerva_bcb.pdf, vignettes/adSplit/inst/doc/tr_2005_02.pdf vignetteTitles: bcb_logo.pdf, minerva_bcb.pdf, Annotation-Driven Clustering hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/adSplit/inst/doc/tr_2005_02.R Package: affxparser Version: 1.30.2 Depends: R (>= 2.6.0) Suggests: R.utils (>= 1.19.3), AffymetrixDataTestFiles License: LGPL (>= 2) Archs: i386, x64 Title: Affymetrix File Parsing SDK Description: Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure. biocViews: Infrastructure, DataImport Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper Daniel Hansen, Martin Morgan Maintainer: Kasper Daniel Hansen MD5sum: f0197d2ce532839004ebdcbf0b7fc5de source.ver: src/contrib/affxparser_1.30.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/affxparser_1.30.2.zip win64.binary.ver: bin/windows64/contrib/2.15/affxparser_1.30.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affxparser_1.30.2.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS, pdInfoBuilder, rMAT, Starr importsMe: affyILM, AffyTiling, cn.farms, GeneRegionScan, ITALICS, oligo, rMAT Package: affy Version: 1.36.1 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: BiocGenerics, Biobase, affyio (>= 1.13.3), BiocInstaller, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools License: LGPL (>= 2.0) Archs: i386, x64 Title: Methods for Affymetrix Oligonucleotide Arrays Description: The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it. biocViews: Microarray, OneChannel, Preprocessing Author: Rafael A. Irizarry , Laurent Gautier , Benjamin Milo Bolstad , and Crispin Miller with contributions from Magnus Astrand , Leslie M. Cope , Robert Gentleman, Jeff Gentry, Conrad Halling , Wolfgang Huber, James MacDonald , Benjamin I. P. Rubinstein, Christopher Workman , John Zhang Maintainer: Rafael A. Irizarry MD5sum: ce1da25547feda90c5432b61c2ee9fc9 source.ver: src/contrib/affy_1.36.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/affy_1.36.1.zip win64.binary.ver: bin/windows64/contrib/2.15/affy_1.36.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affy_1.36.1.tgz vignettes: vignettes/affy/inst/doc/affy.pdf, vignettes/affy/inst/doc/builtinMethods.pdf, vignettes/affy/inst/doc/customMethods.pdf, vignettes/affy/inst/doc/vim.pdf vignetteTitles: 1. Primer, 2. Built-in Processing Methods, 3. Custom Processing Methods, 4. Import Methods hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affy/inst/doc/affy.R, vignettes/affy/inst/doc/builtinMethods.R, vignettes/affy/inst/doc/customMethods.R, vignettes/affy/inst/doc/vim.R dependsOnMe: affyContam, affycoretools, AffyExpress, affylmGUI, affyPara, affypdnn, affyPLM, affyQCReport, AffyRNADegradation, altcdfenvs, arrayMvout, ArrayTools, bgx, Cormotif, dualKS, ExiMiR, farms, frmaTools, gcrma, LMGene, logitT, maDB, maskBAD, MLP, panp, plw, puma, qpcrNorm, ReadqPCR, RefPlus, rHVDM, RPA, simpleaffy, sscore, Starr, webbioc importsMe: affyILM, affyQCReport, AffyTiling, ArrayExpress, arrayQualityMetrics, ArrayTools, ChIPXpress, Cormotif, farms, ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, lumi, makecdfenv, MSnbase, plier, plw, puma, pvac, simpleaffy, tilingArray, TurboNorm, virtualArray, vsn, waveTiling suggestsMe: AnnotationForge, beadarray, beadarraySNP, BiocCaseStudies, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, ExpressionView, factDesign, ffpe, GeneRegionScan, limma, made4, oneChannelGUI, PREDA, siggenes, TurboNorm Package: affycomp Version: 1.34.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) Title: Graphics Toolbox for Assessment of Affymetrix Expression Measures Description: The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. biocViews: OneChannel, Microarray, Preprocessing Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Rafael A. Irizarry MD5sum: 2dfa3507781f8db9656253aafb3f4cf1 source.ver: src/contrib/affycomp_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affycomp_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affycomp_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affycomp_1.34.0.tgz vignettes: vignettes/affycomp/inst/doc/affycomp.pdf vignetteTitles: affycomp primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affycomp/inst/doc/affycomp.R Package: AffyCompatible Version: 1.18.2 Depends: R (>= 2.7.0), XML (>= 2.8-1), RCurl (>= 0.8-1), methods Imports: Biostrings License: Artistic-2.0 Title: Affymetrix GeneChip software compatibility Description: This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files. biocViews: Infrastructure, Microarray, OneChannel Author: Martin Morgan, Robert Gentleman Maintainer: Martin Morgan MD5sum: 9d455b8c8ea154308cfc4ddb99710a4d source.ver: src/contrib/AffyCompatible_1.18.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffyCompatible_1.18.2.zip win64.binary.ver: bin/windows64/contrib/2.15/AffyCompatible_1.18.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffyCompatible_1.18.2.tgz vignettes: vignettes/AffyCompatible/inst/doc/MAGEAndARR.pdf, vignettes/AffyCompatible/inst/doc/NetAffxResource.pdf vignetteTitles: Retrieving MAGE and ARR sample attributes, Annotation retrieval with NetAffxResource hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AffyCompatible/inst/doc/MAGEAndARR.R, vignettes/AffyCompatible/inst/doc/NetAffxResource.R importsMe: IdMappingRetrieval Package: affyContam Version: 1.16.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata License: Artistic-2.0 Title: structured corruption of affymetrix cel file data Description: structured corruption of cel file data to demonstrate QA effectiveness biocViews: Infrastructure, Bioinformatics Author: V. Carey Maintainer: V. Carey MD5sum: c7bd1ea7e9c37cc6d39facd5c08f7e73 source.ver: src/contrib/affyContam_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyContam_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyContam_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyContam_1.16.0.tgz vignettes: vignettes/affyContam/inst/doc/affyContam.pdf vignetteTitles: affy contamination tools hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affyContam/inst/doc/affyContam.R Package: affycoretools Version: 1.30.0 Depends: affy, Biobase, GO.db, KEGG.db Imports: biomaRt, limma, GOstats, annotate, annaffy, genefilter, gcrma, splines, xtable, AnnotationDbi, lattice, gplots Suggests: affydata, hgfocuscdf, rgl License: Artistic-2.0 Title: Functions useful for those doing repetitive analyses with Affymetrix GeneChips. Description: Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see. biocViews: ReportWriting, Microarray, OneChannel, GeneExpression Author: James W. MacDonald Maintainer: James W. MacDonald MD5sum: 254b996ba2583859e77ac294b94b1b3c source.ver: src/contrib/affycoretools_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affycoretools_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affycoretools_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affycoretools_1.30.0.tgz vignettes: vignettes/affycoretools/inst/doc/affycoretools_biomaRt.pdf, vignettes/affycoretools/inst/doc/affycoretools.pdf vignetteTitles: affycoretools biomaRt Integration, affycoretools Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affycoretools/inst/doc/affycoretools_biomaRt.R, vignettes/affycoretools/inst/doc/affycoretools.R suggestsMe: Agi4x44PreProcess Package: AffyExpress Version: 1.24.0 Depends: R (>= 2.10), affy (>= 1.23.4), limma Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma License: LGPL Title: Affymetrix Quality Assessment and Analysis Tool Description: The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Bioinformatics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Xiwei Wu , Xuejun Arthur Li Maintainer: Xuejun Arthur Li MD5sum: 8b073cd0cf5e47c2eb9e984f07b1b93a source.ver: src/contrib/AffyExpress_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffyExpress_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AffyExpress_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffyExpress_1.24.0.tgz vignettes: vignettes/AffyExpress/inst/doc/AffyExpress.pdf vignetteTitles: 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AffyExpress/inst/doc/AffyExpress.R Package: affyILM Version: 1.10.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, methods, Biobase Suggests: AffymetrixDataTestFiles License: GPL version 3 Title: Linear Model of background subtraction and the Langmuir isotherm Description: affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model. biocViews: Microarray, OneChannel, Preprocessing Author: K. Myriam Kroll, Fabrice Berger, Gerard Barkema, Enrico Carlon Maintainer: Myriam Kroll and Fabrice Berger MD5sum: 2aef75dba97bb45afae4c02e87687251 source.ver: src/contrib/affyILM_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyILM_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyILM_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyILM_1.10.0.tgz vignettes: vignettes/affyILM/inst/doc/affyILM.pdf vignetteTitles: affyILM1.3.0 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affyILM/inst/doc/affyILM.R Package: affyio Version: 1.26.0 Depends: R (>= 2.6.0), methods Imports: zlibbioc License: LGPL (>= 2) Archs: i386, x64 Title: Tools for parsing Affymetrix data files Description: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats. biocViews: Microarray, DataImport, Infrastructure Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad MD5sum: 49f79ea18618b82e1babfd146faabf68 source.ver: src/contrib/affyio_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyio_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyio_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyio_1.26.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: affylmGUI, sscore importsMe: affy, crlmm, gcrma, oligo, oligoClasses suggestsMe: BufferedMatrixMethods Package: affylmGUI Version: 1.32.0 Depends: limma, tcltk, affy, BiocInstaller, affyio Suggests: tkrplot, affyPLM, R2HTML, xtable License: LGPL Title: GUI for affy analysis using limma package Description: A Graphical User Interface for affy analysis using the limma Microarray package biocViews: Microarray, OneChannel, DataImport, QualityControl, Preprocessing, Bioinformatics, DifferentialExpression, MultipleComparisons, GUI Author: James Wettenhall and Ken Simpson Division of Genetics and Bioinformatics, WEHI. Maintainer: Keith Satterley URL: http://bioinf.wehi.edu.au/affylmGUI/ MD5sum: f94f6e0f0be51b2675dcb7074a52ed36 source.ver: src/contrib/affylmGUI_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affylmGUI_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affylmGUI_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affylmGUI_1.32.0.tgz vignettes: vignettes/affylmGUI/inst/doc/affylmGUI.pdf, vignettes/affylmGUI/inst/doc/extract.pdf vignetteTitles: affylmGUI Vignette, Extracting affy and limma objects from affylmGUI files hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affylmGUI/inst/doc/affylmGUI.R, vignettes/affylmGUI/inst/doc/extract.R htmlDocs: vignettes/affylmGUI/inst/doc/about.html, vignettes/affylmGUI/inst/doc/CustMenu.html, vignettes/affylmGUI/inst/doc/index.html, vignettes/affylmGUI/inst/doc/windowsFocus.html dependsOnMe: oneChannelGUI Package: affyPara Version: 1.18.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0), aplpack (>= 1.1.1) Suggests: affydata Enhances: affy License: GPL-3 Title: Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays Description: The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data. biocViews: Microarray, Preprocessing Author: Markus Schmidberger , Esmeralda Vicedo , Ulrich Mansmann Maintainer: Markus Schmidberger URL: http://www.ibe.med.uni-muenchen.de MD5sum: 57b459595f0764bdba80f84e595b8efa source.ver: src/contrib/affyPara_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyPara_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyPara_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyPara_1.18.0.tgz vignettes: vignettes/affyPara/inst/doc/affyPara.pdf, vignettes/affyPara/inst/doc/vsnStudy.pdf vignetteTitles: Parallelized affy functions for preprocessing, Simulation Study for VSN Add-On Normalization and Subsample Size hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affyPara/inst/doc/affyPara.R, vignettes/affyPara/inst/doc/vsnStudy.R Package: affypdnn Version: 1.32.0 Depends: R (>= 2.13.0), affy (>= 1.5) Suggests: affydata, hgu95av2probe License: LGPL Title: Probe Dependent Nearest Neighbours (PDNN) for the affy package Description: The package contains functions to perform the PDNN method described by Li Zhang et al. biocViews: OneChannel, Microarray, Preprocessing Author: H. Bjorn Nielsen and Laurent Gautier (Many thanks to Li Zhang early communications about the existence of the PDNN program and related publications). Maintainer: Laurent Gautier MD5sum: df3cf0a6b6da79843c3e20338585c4c9 source.ver: src/contrib/affypdnn_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affypdnn_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affypdnn_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affypdnn_1.32.0.tgz vignettes: vignettes/affypdnn/inst/doc/affypdnn.pdf vignetteTitles: affypdnn hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affypdnn/inst/doc/affypdnn.R Package: affyPLM Version: 1.34.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0), Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1) Imports: BiocGenerics, zlibbioc, graphics, grDevices, methods LinkingTo: preprocessCore Suggests: affydata, MASS License: GPL (>= 2) Archs: i386, x64 Title: Methods for fitting probe-level models Description: A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools. biocViews: Microarray, OneChannel, Preprocessing, QualityControl Author: Ben Bolstad Maintainer: Ben Bolstad URL: http://bmbolstad.com MD5sum: 95793fc13d81edf7db5e11dd49348302 source.ver: src/contrib/affyPLM_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyPLM_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyPLM_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyPLM_1.34.0.tgz vignettes: vignettes/affyPLM/inst/doc/AffyExtensions.pdf, vignettes/affyPLM/inst/doc/MAplots.pdf, vignettes/affyPLM/inst/doc/QualityAssess.pdf, vignettes/affyPLM/inst/doc/ThreeStep.pdf vignetteTitles: affyPLM: Fitting Probe Level Models, affyPLM: Advanced use of the MAplot function, affyPLM: Model Based QC Assessment of Affymetrix GeneChips, affyPLM: the threestep function hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affyPLM/inst/doc/AffyExtensions.R, vignettes/affyPLM/inst/doc/MAplots.R, vignettes/affyPLM/inst/doc/QualityAssess.R, vignettes/affyPLM/inst/doc/ThreeStep.R dependsOnMe: RefPlus importsMe: affyQCReport, arrayQualityMetrics, virtualArray suggestsMe: AffyExpress, affylmGUI, arrayMvout, ArrayTools, BiocCaseStudies, BiocGenerics, frmaTools, ggbio, metahdep, oneChannelGUI Package: affyQCReport Version: 1.36.0 Depends: Biobase (>= 1.13.16), affy, lattice Imports: affy, affyPLM, Biobase, genefilter, graphics, grDevices, lattice, RColorBrewer, simpleaffy, stats, utils, xtable Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1) License: LGPL (>= 2) Title: QC Report Generation for affyBatch objects Description: This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. biocViews: Microarray,OneChannel,QualityControl Author: Craig Parman , Conrad Halling , Robert Gentleman Maintainer: Craig Parman MD5sum: 9712a8f30e08dc7798ac9601ec297a06 source.ver: src/contrib/affyQCReport_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyQCReport_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyQCReport_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyQCReport_1.36.0.tgz vignettes: vignettes/affyQCReport/inst/doc/affyQCReport.pdf vignetteTitles: affyQCReport: Methods for Generating Affymetrix QC Reports hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affyQCReport/inst/doc/affyQCReport.R suggestsMe: BiocCaseStudies Package: AffyRNADegradation Version: 1.4.0 Depends: R (>= 2.9.0), methods, affy Suggests: AmpAffyExample License: GPL-2 Title: Analyze and correct probe positional bias in microarray data due to RNA degradation Description: The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation. biocViews: GeneExpression, Microarray, OneChannel, Preprocessing, QualityControl, Bioinformatics Author: Mario Fasold Maintainer: Mario Fasold MD5sum: 7f23aa06335b16cd04279a9cce31ecf5 source.ver: src/contrib/AffyRNADegradation_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffyRNADegradation_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AffyRNADegradation_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffyRNADegradation_1.4.0.tgz vignettes: vignettes/AffyRNADegradation/inst/doc/vignette.pdf vignetteTitles: AffyRNADegradation Example hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AffyRNADegradation/inst/doc/vignette.R Package: AffyTiling Version: 1.16.1 Depends: R (>= 2.6) Imports: affxparser, affy (>= 1.16), stats, utils, preprocessCore License: GPL (>= 2) Archs: i386, x64 Title: Easy extraction of individual probes in Affymetrix tiling arrays Description: This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays. biocViews: Microarray, Preprocessing Author: Charles G. Danko Maintainer: Charles G. Danko MD5sum: bc48c08feba49130a1702ed2af4267bc source.ver: src/contrib/AffyTiling_1.16.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffyTiling_1.16.1.zip win64.binary.ver: bin/windows64/contrib/2.15/AffyTiling_1.16.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffyTiling_1.16.1.tgz vignettes: vignettes/AffyTiling/inst/doc/AffyTiling.pdf vignetteTitles: AffyTiling hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AffyTiling/inst/doc/AffyTiling.R Package: AGDEX Version: 1.6.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL Version 2 or later Title: Agreement of Differential Expression Analysis Description: A tool to evaluate agreement of differential expression for cross-species genomics biocViews: Microarray, Genetics, Bioinformatics, GeneExpression Author: Stan Pounds ; Cuilan Lani Gao Maintainer: Cuilan lani Gao MD5sum: 84b585c15fbeb006c747284decd87910 source.ver: src/contrib/AGDEX_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AGDEX_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AGDEX_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AGDEX_1.6.0.tgz vignettes: vignettes/AGDEX/inst/doc/AGDEX.pdf vignetteTitles: AGDEX.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AGDEX/inst/doc/AGDEX.R Package: Agi4x44PreProcess Version: 1.18.0 Depends: R (>= 2.10), Biobase, limma, annotate, genefilter Suggests: vsn, affycoretools, hgug4112a.db, GO.db, marray, gplots, gtools, gdata License: GPL-3 Title: PreProcessing of Agilent 4x44 array data Description: Preprocessing of Agilent 4x44 array data biocViews: Microarray, OneChannel, Preprocessing Author: Pedro Lopez-Romero Maintainer: Pedro Lopez-Romero MD5sum: 8fe40f90ba22882438174504e74bde8a source.ver: src/contrib/Agi4x44PreProcess_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Agi4x44PreProcess_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Agi4x44PreProcess_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Agi4x44PreProcess_1.18.0.tgz vignettes: vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf vignetteTitles: Agi4x44PreProcess hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.R Package: agilp Version: 3.0.0 Depends: R (>= 2.14.0) License: GPL-3 Title: Agilent expression array processing package Description: provides a pipeline for the low-level analysis of gene expression microarray data, primarily Agilent data Author: Benny Chain Maintainer: Benny Chain MD5sum: c7c0cd6a36b0902375ef063bff77fd22 source.ver: src/contrib/agilp_3.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/agilp_3.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/agilp_3.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/agilp_3.0.0.tgz vignettes: vignettes/agilp/inst/doc/agilp_manual.pdf vignetteTitles: An R Package for processing expression microarray data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/agilp/inst/doc/agilp_manual.R Package: AgiMicroRna Version: 2.8.0 Depends: R (>= 2.10),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 Title: Processing and Differential Expression Analysis of Agilent microRNA chips Description: Processing and Analysis of Agilent microRNA data biocViews: Microarray,AgilentChip,OneChannel,Preprocessing,DifferentialExpression,Bioinformatics Author: Pedro Lopez-Romero Maintainer: Pedro Lopez-Romero MD5sum: 0b7ad6d12deaddd9e5f6470165fcfda4 source.ver: src/contrib/AgiMicroRna_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AgiMicroRna_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AgiMicroRna_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AgiMicroRna_2.8.0.tgz vignettes: vignettes/AgiMicroRna/inst/doc/AgiMicroRna.pdf vignetteTitles: AgiMicroRna hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AgiMicroRna/inst/doc/AgiMicroRna.R Package: altcdfenvs Version: 2.20.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) Title: alternative CDF environments (aka probeset mappings) Description: Convenience data structures and functions to handle cdfenvs biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Annotation, ProprietaryPlatforms, Transcription Author: Laurent Gautier Maintainer: Laurent Gautier MD5sum: ef7103c545763cd1c00dc0d269944b51 source.ver: src/contrib/altcdfenvs_2.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/altcdfenvs_2.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/altcdfenvs_2.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/altcdfenvs_2.20.0.tgz vignettes: vignettes/altcdfenvs/inst/doc/altcdfenvs.pdf, vignettes/altcdfenvs/inst/doc/modify.pdf, vignettes/altcdfenvs/inst/doc/ngenomeschips.pdf vignetteTitles: altcdfenvs, affy primer, affy primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/altcdfenvs/inst/doc/altcdfenvs.R, vignettes/altcdfenvs/inst/doc/modify.R, vignettes/altcdfenvs/inst/doc/ngenomeschips.R importsMe: Harshlight Package: annaffy Version: 1.30.0 Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db Imports: AnnotationDbi (>= 0.1.15) Suggests: hgu95av2.db, multtest, tcltk License: LGPL Title: Annotation tools for Affymetrix biological metadata Description: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. biocViews: OneChannel, Microarray, Annotation, GO, Pathways, ReportWriting Author: Colin A. Smith Maintainer: Colin A. Smith MD5sum: 706772d7ae0b91168fbf826172af773c source.ver: src/contrib/annaffy_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/annaffy_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/annaffy_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/annaffy_1.30.0.tgz vignettes: vignettes/annaffy/inst/doc/annaffy.pdf vignetteTitles: annaffy Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/annaffy/inst/doc/annaffy.R dependsOnMe: a4Base, a4Reporting, PGSEA, webbioc importsMe: affycoretools suggestsMe: AffyExpress, ArrayTools, BiocCaseStudies, maDB Package: annmap Version: 1.0.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson License: GPL-2 Title: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis. Description: annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. biocViews: Annotation, Bioinformatics, Microarray, OneChannel, ReportWriting, Transcription, Visualization Author: Tim Yates Maintainer: Tim Yates URL: http://annmap.picr.man.ac.uk MD5sum: 1ba2dc5cb5cd9d98894ee542ba55ae21 source.ver: src/contrib/annmap_1.0.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/annmap_1.0.0.tgz vignettes: vignettes/annmap/inst/doc/annmap.pdf, vignettes/annmap/inst/doc/cookbook.pdf, vignettes/annmap/inst/doc/INSTALL.pdf vignetteTitles: annmap primer, The Annmap Cookbook, annmap installation instruction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/annmap/inst/doc/annmap.R, vignettes/annmap/inst/doc/cookbook.R, vignettes/annmap/inst/doc/INSTALL.R Package: annotate Version: 1.36.0 Depends: R (>= 2.10), AnnotationDbi (>= 0.1.15) Imports: Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats, methods, XML (>= 0.92-2), BiocGenerics (>= 0.1.13) Suggests: Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.25.10), rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, XML (>= 0.92-2), org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, License: Artistic-2.0 Title: Annotation for microarrays Description: Using R enviroments for annotation. biocViews: Annotation, Pathways, GO Author: R. Gentleman Maintainer: Bioconductor Package Maintainer MD5sum: d10a9c0482613386d825d1e1e1655260 source.ver: src/contrib/annotate_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/annotate_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/annotate_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/annotate_1.36.0.tgz vignettes: vignettes/annotate/inst/doc/annotate.pdf, vignettes/annotate/inst/doc/chromLoc.pdf, vignettes/annotate/inst/doc/GOusage.pdf, vignettes/annotate/inst/doc/prettyOutput.pdf, vignettes/annotate/inst/doc/query.pdf, vignettes/annotate/inst/doc/useDataPkgs.pdf, vignettes/annotate/inst/doc/useHomology.pdf, vignettes/annotate/inst/doc/useProbeInfo.pdf vignetteTitles: Annotation Overview, HowTo: use chromosomal information, Basic GO Usage, HowTo: Get HTML Output, HOWTO: Use the online query tools, Using Data Packages, Using the homology package, Using Affymetrix Probe Level Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/annotate/inst/doc/annotate.R, vignettes/annotate/inst/doc/chromLoc.R, vignettes/annotate/inst/doc/GOusage.R, vignettes/annotate/inst/doc/prettyOutput.R, vignettes/annotate/inst/doc/query.R, vignettes/annotate/inst/doc/useDataPkgs.R, vignettes/annotate/inst/doc/useHomology.R, vignettes/annotate/inst/doc/useProbeInfo.R dependsOnMe: Agi4x44PreProcess, ChromHeatMap, GeneAnswers, geneplotter, GSEABase, idiogram, macat, MLInterfaces, PCpheno, phenoTest, PREDA, RpsiXML, safe, ScISI importsMe: affycoretools, Category, categoryCompare, ChromHeatMap, codelink, gCMAP, GeneAnswers, genefilter, GeneGroupAnalysis, geneplotter, GlobalAncova, globaltest, GOstats, GSEABase, lumi, methyAnalysis, methylumi, phenoTest, qpgraph, safe, ScISI, splicegear, tigre suggestsMe: BiocCaseStudies, biomaRt, geneplotter, GlobalAncova, globaltest, GOstats, GSEAlm, maigesPack, MLP, oneChannelGUI, puma, siggenes, tigre Package: AnnotationDbi Version: 1.20.7 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.1.13), Biobase (>= 1.17.0) Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase, IRanges Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, seqnames.db, reactome.db, AnnotationForge License: Artistic-2.0 Title: Annotation Database Interface Description: Provides user interface and database connection code for annotation data packages using SQLite data storage. biocViews: Annotation, Infrastructure Author: Herve Pages, Marc Carlson, Seth Falcon, Nianhua Li Maintainer: Bioconductor Package Maintainer MD5sum: 05c014c2b2b45e40d65706b09f1bb1a2 source.ver: src/contrib/AnnotationDbi_1.20.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/AnnotationDbi_1.20.7.zip win64.binary.ver: bin/windows64/contrib/2.15/AnnotationDbi_1.20.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AnnotationDbi_1.20.7.tgz vignettes: vignettes/AnnotationDbi/inst/doc/AnnotationDbi.pdf, vignettes/AnnotationDbi/inst/doc/databaseTypes.pdf, vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf vignetteTitles: How to use bimaps from the ".db" annotation packages, databaseTypes.pdf, AnnotationDbi: Introduction To Bioconductor Annotation Packages hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AnnotationDbi/inst/doc/AnnotationDbi.R, vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.R, vignettes/AnnotationDbi/inst/doc/makeProbePackage.R, vignettes/AnnotationDbi/inst/doc/NewSchema.R, vignettes/AnnotationDbi/inst/doc/SQLForge.R dependsOnMe: a4Base, a4Preproc, annotate, AnnotationForge, AnnotationFuncs, attract, Category, categoryCompare, ChromHeatMap, eisa, ExpressionView, GenomicFeatures, GOFunction, goProfiles, MLP, OrganismDbi, PADOG, PAnnBuilder, pathRender, PGSEA, Resourcerer, RpsiXML, topGO importsMe: adSplit, affycoretools, annaffy, annotate, attract, beadarray, BioNet, CancerMutationAnalysis, Category, categoryCompare, ChIPpeakAnno, ChromHeatMap, clusterProfiler, CoCiteStats, domainsignatures, DOSE, ExpressionView, FunciSNP, genefilter, GeneGroupAnalysis, geneplotter, GGBase, GGtools, GlobalAncova, globaltest, GOFunction, GOSemSim, goseq, GOstats, goTools, graphite, GSEABase, Gviz, HTSanalyzeR, KEGGprofile, lumi, methyAnalysis, methylumi, MiRaGE, OrganismDbi, PADOG, PAnnBuilder, pcaGoPromoter, PCpheno, phenoTest, qpgraph, ReactomePA, REDseq, safe, ScISI, SLGI, tigre, topGO, VariantAnnotation, virtualArray suggestsMe: BiocCaseStudies, BiocGenerics, GeneAnswers, GeneRegionScan, MmPalateMiRNA, oneChannelGUI, sigPathway Package: AnnotationForge Version: 1.0.3 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.1.13), Biobase (>= 1.17.0), AnnotationDbi (>= 1.19.15), org.Hs.eg.db Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), XML, RCurl, hgu95av2.db, human.db0, affy, Homo.sapiens, hom.Hs.inp.db, GO.db License: Artistic-2.0 Title: Code for Building Annotation Database Packages Description: Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi. biocViews: Annotation, Infrastructure Author: Marc Carlson, Herve Pages Maintainer: Bioconductor Package Maintainer MD5sum: 2a0080456452385248b864f8376e8977 source.ver: src/contrib/AnnotationForge_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/AnnotationForge_1.0.3.zip win64.binary.ver: bin/windows64/contrib/2.15/AnnotationForge_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AnnotationForge_1.0.3.tgz vignettes: vignettes/AnnotationForge/inst/doc/makeProbePackage.pdf, vignettes/AnnotationForge/inst/doc/NewSchema.pdf, vignettes/AnnotationForge/inst/doc/SQLForge.pdf vignetteTitles: Creating probe packages, Creating an annotation package with a new database schema, SQLForge: An easy way to create a new annotation package with a standard database schema. hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AnnotationForge/inst/doc/makeProbePackage.R, vignettes/AnnotationForge/inst/doc/NewSchema.R, vignettes/AnnotationForge/inst/doc/SQLForge.R importsMe: GOstats suggestsMe: AnnotationDbi Package: AnnotationFuncs Version: 1.8.0 Depends: R (>= 2.7.0), AnnotationDbi Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db License: GPL-2 Title: Annotation translation functions Description: Functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. org.Bt.eg.db). biocViews: AnnotationData, Software Author: Stefan McKinnon Edwards Maintainer: Stefan McKinnon Edwards URL: http://www.iysik.com/index.php?page=annotation-functions MD5sum: 83295b8f214366c259f012d053c0f798 source.ver: src/contrib/AnnotationFuncs_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AnnotationFuncs_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AnnotationFuncs_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AnnotationFuncs_1.8.0.tgz vignettes: vignettes/AnnotationFuncs/inst/doc/AnnotationFuncsUserguide.pdf vignetteTitles: Annotation mapping functions hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: annotationTools Version: 1.32.0 Imports: Biobase, stats License: GPL Title: Annotate microarrays and perform cross-species gene expression analyses using flat file databases. Description: Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). biocViews: Microarray, Annotation Author: Alexandre Kuhn Maintainer: Alexandre Kuhn MD5sum: 47a2f46e43050363afe95632de17dca3 source.ver: src/contrib/annotationTools_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/annotationTools_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/annotationTools_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/annotationTools_1.32.0.tgz vignettes: vignettes/annotationTools/inst/doc/annotationTools.pdf vignetteTitles: annotationTools Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/annotationTools/inst/doc/annotationTools.R Package: anota Version: 1.6.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 Title: ANalysis Of Translational Activity (ANOTA). Description: Genome wide studies of translational control is emerging as a tool to study verious biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallell the library performs a number of tests to assure that the data set is suitable for such analysis. biocViews: GeneExpression, DifferentialExpression, Microarray, HighThroughputSequencing Author: Ola Larsson , Nahum Sonenberg , Robert Nadon Maintainer: Ola Larsson MD5sum: 425d005789afaeeccd0f1380867e4aff source.ver: src/contrib/anota_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/anota_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/anota_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/anota_1.6.0.tgz vignettes: vignettes/anota/inst/doc/anota.pdf vignetteTitles: ANalysis Of Translational Activity (anota) hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/anota/inst/doc/anota.R Package: apComplex Version: 2.24.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL Title: Estimate protein complex membership using AP-MS protein data Description: Functions to estimate a bipartite graph of protein complex membership using AP-MS data. biocViews: NetworkInference, MassSpectrometry, GraphsAndNetworks Author: Denise Scholtens Maintainer: Denise Scholtens MD5sum: 4e6fa1f58f69569f643f6f4bad418b7b source.ver: src/contrib/apComplex_2.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/apComplex_2.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/apComplex_2.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/apComplex_2.24.0.tgz vignettes: vignettes/apComplex/inst/doc/apComplex.pdf vignetteTitles: apComplex hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/apComplex/inst/doc/apComplex.R dependsOnMe: ScISI suggestsMe: BiocCaseStudies Package: aroma.light Version: 1.28.0 Depends: R (>= 2.10.0), matrixStats (>= 0.5.3) Imports: R.methodsS3 (>= 1.4.2) Suggests: R.oo (>= 1.9.9), R.utils (>= 1.16.2), princurve (>= 1.1-11) License: GPL (>= 2) Title: Light-weight methods for normalization and visualization of microarray data using only basic R data types Description: Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. biocViews: Infrastructure, Microarray, OneChannel, TwoChannel, MultiChannel, Visualization, Preprocessing Author: Henrik Bengtsson Maintainer: Henrik Bengtsson URL: http://www.aroma-project.org/ MD5sum: 69dabbb219ddad3fbb1a8ece946956d8 source.ver: src/contrib/aroma.light_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/aroma.light_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/aroma.light_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/aroma.light_1.28.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: EDASeq Package: ArrayExpress Version: 1.18.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, affy, limma License: Artistic-2.0 Title: Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet Description: Access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet biocViews: Microarray, DataImport, OneChannel, TwoChannel Author: Audrey Kauffmann, Ibrahim Emam Maintainer: Ibrahim Emam MD5sum: 49e003ae79249d566d6174eb5517b2c6 source.ver: src/contrib/ArrayExpress_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ArrayExpress_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ArrayExpress_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ArrayExpress_1.18.0.tgz vignettes: vignettes/ArrayExpress/inst/doc/ArrayExpress.pdf vignetteTitles: ArrayExpress: Import and convert ArrayExpress data sets into R object hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ArrayExpress/inst/doc/ArrayExpress.R Package: ArrayExpressHTS Version: 1.8.0 Depends: sampling, Rsamtools (>= 1.3.32), snow Imports: Biobase, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges, R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils LinkingTo: Rsamtools License: Artistic License 2.0 Title: ArrayExpress High Throughput Sequencing Processing Pipeline Description: RNA-Seq processing pipeline for public ArrayExpress experiments or local datasets biocViews: RNAseq, Sequencing, HighThroughputSequencing Author: Angela Goncalves, Andrew Tikhonov Maintainer: Angela Goncalves , Andrew Tikhonov MD5sum: 6b3eabc698e67f45d32088f8833d9555 source.ver: src/contrib/ArrayExpressHTS_1.8.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ArrayExpressHTS_1.8.0.tgz vignettes: vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.pdf vignetteTitles: ArrayExpressHTS: RNA-Seq Pipeline for transcription profiling experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.R Package: arrayMvout Version: 1.16.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy, lumi Imports: simpleaffy, mdqc, affyContam, Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 Title: multivariate outlier detection for expression array QA Description: This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate biocViews: Infrastructure, Bioinformatics, Microarray, QualityControl Author: Z. Gao, A. Asare, R. Wang, V. Carey Maintainer: V. Carey MD5sum: 47eb77a7982309573d7c947c4f992266 source.ver: src/contrib/arrayMvout_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/arrayMvout_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/arrayMvout_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/arrayMvout_1.16.0.tgz vignettes: vignettes/arrayMvout/inst/doc/arrayMvout-asdad.pdf, vignettes/arrayMvout/inst/doc/arrayMvout-lkadas.pdf, vignettes/arrayMvout/inst/doc/arrayMvout-lkda.pdf, vignettes/arrayMvout/inst/doc/arrayMvout.pdf vignetteTitles: arrayMvout-asdad.pdf, arrayMvout-lkadas.pdf, arrayMvout-lkda.pdf, arrayMvout -- multivariate outlier algorithm for expression arrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/arrayMvout/inst/doc/arrayMvout.R Package: arrayQuality Version: 1.36.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL Title: Assessing array quality on spotted arrays Description: Functions for performing print-run and array level quality assessment. biocViews: Microarray,TwoChannel,QualityControl,Visualization Author: Agnes Paquet and Jean Yee Hwa Yang Maintainer: Agnes Paquet URL: http://arrays.ucsf.edu/ MD5sum: 51c331a456f32b31c34499ae9bb478f4 source.ver: src/contrib/arrayQuality_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/arrayQuality_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/arrayQuality_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/arrayQuality_1.36.0.tgz vignettes: vignettes/arrayQuality/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/arrayQuality/inst/doc/basicQuality.html, vignettes/arrayQuality/inst/doc/customQuality.html, vignettes/arrayQuality/inst/doc/index.html, vignettes/arrayQuality/inst/doc/print-runQC.html Package: arrayQualityMetrics Version: 3.14.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, Cairo (>= 1.4-6), genefilter, graphics, grDevices, grid, Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, simpleaffy, stats, SVGAnnotation (>= 0.9-0), utils, vsn (>= 3.23.3), XML Suggests: ALLMLL, CCl4 License: LGPL (>= 2) Title: Quality metrics on microarray data sets Description: This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Report contain both general and platform-specific sections. Both one and two color array platforms are supported. biocViews: Microarray, QualityControl, OneChannel, TwoChannel, ReportWriting Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann MD5sum: dd80d40e0831282d32675d80cc3646ac source.ver: src/contrib/arrayQualityMetrics_3.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/arrayQualityMetrics_3.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/arrayQualityMetrics_3.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/arrayQualityMetrics_3.14.0.tgz vignettes: vignettes/arrayQualityMetrics/inst/doc/aqm.pdf, vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.pdf vignetteTitles: Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output, Introduction: microarray quality assessment with arrayQualityMetrics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/arrayQualityMetrics/inst/doc/aqm.R, vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.R Package: ArrayTools Version: 1.18.0 Depends: R (>= 2.7.0), affy (>= 1.23.4), Biobase (>= 2.5.5), methods Imports: affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db License: LGPL (>= 2.0) Title: geneChip Analysis Package Description: This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases. biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Statistics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Xiwei Wu, Arthur Li Maintainer: Arthur Li MD5sum: 691e6103836ddab3b4bca90950c8ae0f source.ver: src/contrib/ArrayTools_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ArrayTools_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ArrayTools_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ArrayTools_1.18.0.tgz vignettes: vignettes/ArrayTools/inst/doc/ArrayTools.pdf vignetteTitles: 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ArrayTools/inst/doc/ArrayTools.R Package: ASEB Version: 1.2.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) Archs: i386, x64 Title: Predict Acetylated Lysine Sites Description: ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT-family. biocViews: Proteomics Author: Likun Wang and Tingting Li . Maintainer: Likun Wang MD5sum: f0e0b594657203e2e52bfb54d94cfce7 source.ver: src/contrib/ASEB_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ASEB_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ASEB_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ASEB_1.2.0.tgz vignettes: vignettes/ASEB/inst/doc/ASEB.pdf vignetteTitles: ASEB hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ASEB/inst/doc/ASEB.R Package: attract Version: 1.10.0 Depends: R (>= 2.10.0), AnnotationDbi, KEGG.db, limma, cluster, GOstats, graphics, methods, stats Imports: Biobase, AnnotationDbi, KEGG.db, limma, cluster, GOstats, graphics, methods, stats Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) Title: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape Description: This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression. biocViews: Statistics, GeneExpression Author: Jessica Mar Maintainer: Jessica Mar MD5sum: a55e0be79006dd997d05196322858119 source.ver: src/contrib/attract_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/attract_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/attract_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/attract_1.10.0.tgz vignettes: vignettes/attract/inst/doc/attract.pdf vignetteTitles: Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/attract/inst/doc/attract.R Package: BAC Version: 1.18.0 Depends: R (>= 2.10) License: Artistic-2.0 Archs: i386, x64 Title: Bayesian Analysis of Chip-chip experiment Description: This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments biocViews: Microarray,Transcription,Bioinformatics Author: Raphael Gottardo Maintainer: Raphael Gottardo MD5sum: 391cb6a1daa2cb692e688c446c416d6d source.ver: src/contrib/BAC_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BAC_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BAC_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BAC_1.18.0.tgz vignettes: vignettes/BAC/inst/doc/BAC.pdf vignetteTitles: 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BAC/inst/doc/BAC.R Package: BayesPeak Version: 1.10.0 Depends: R (>= 2.14), IRanges Imports: IRanges, graphics License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Analysis of ChIP-seq Data Description: This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data. biocViews: ChIPseq Author: Christiana Spyrou, Jonathan Cairns, Rory Stark, Andy Lynch, Simon Tavar\\'{e}, Maintainer: Jonathan Cairns MD5sum: 84e920f0e00bb920880d38938e9a067a source.ver: src/contrib/BayesPeak_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BayesPeak_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BayesPeak_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BayesPeak_1.10.0.tgz vignettes: vignettes/BayesPeak/inst/doc/BayesPeak.pdf, vignettes/BayesPeak/inst/doc/regionOFdiag.pdf vignetteTitles: BayesPeak Vignette, regionOFdiag.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BayesPeak/inst/doc/BayesPeak.R Package: baySeq Version: 1.12.0 Depends: R (>= 2.3.0), methods Suggests: snow, edgeR License: GPL-3 Title: Empirical Bayesian analysis of patterns of differential expression in count data Description: This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods. biocViews: Bioinformatics, HighThroughputSequencing, DifferentialExpression, MultipleComparisons, SAGE Author: Thomas J. Hardcastle Maintainer: Thomas J. Hardcastle MD5sum: e473abf0576db5a7374276b0d9d12ca0 source.ver: src/contrib/baySeq_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/baySeq_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/baySeq_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/baySeq_1.12.0.tgz vignettes: vignettes/baySeq/inst/doc/baySeq.pdf vignetteTitles: baySeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/baySeq/inst/doc/baySeq.R dependsOnMe: Rcade, segmentSeq importsMe: segmentSeq suggestsMe: oneChannelGUI Package: BCRANK Version: 1.20.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 Archs: i386, x64 Title: Predicting binding site consensus from ranked DNA sequences Description: Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search biocViews: MotifDiscovery, GeneRegulation Author: Adam Ameur Maintainer: Adam Ameur MD5sum: 9eefe7c2e772c69181fb761ca4b5c144 source.ver: src/contrib/BCRANK_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BCRANK_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BCRANK_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BCRANK_1.20.0.tgz vignettes: vignettes/BCRANK/inst/doc/BCRANK_intro_fig1.pdf, vignettes/BCRANK/inst/doc/BCRANK_intro_fig2.pdf, vignettes/BCRANK/inst/doc/BCRANK.pdf vignetteTitles: BCRANK_intro_fig1.pdf, BCRANK_intro_fig2.pdf, BCRANK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BCRANK/inst/doc/BCRANK.R Package: beadarray Version: 2.8.1 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), methods, ggplot2 Imports: BeadDataPackR, limma, AnnotationDbi, stats4, BiocGenerics, reshape2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra License: GPL-2 Archs: i386, x64 Title: Quality assessment and low-level analysis for Illumina BeadArray data Description: The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. biocViews: Microarray, OneChannel, QualityControl, Preprocessing Author: Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie Maintainer: Mark Dunning MD5sum: 6a4bfbe9c665b3e211ae3f4fd6c63071 source.ver: src/contrib/beadarray_2.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/beadarray_2.8.1.zip win64.binary.ver: bin/windows64/contrib/2.15/beadarray_2.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/beadarray_2.8.1.tgz vignettes: vignettes/beadarray/inst/doc/beadarray.pdf, vignettes/beadarray/inst/doc/beadlevel.pdf, vignettes/beadarray/inst/doc/beadsummary.pdf, vignettes/beadarray/inst/doc/ImageProcessing.pdf vignetteTitles: beadarray.pdf, beadlevel.pdf, beadsummary.pdf, ImageProcessing.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/beadarray/inst/doc/beadarray.R, vignettes/beadarray/inst/doc/beadlevel.R, vignettes/beadarray/inst/doc/beadsummary.R, vignettes/beadarray/inst/doc/ImageProcessing.R importsMe: arrayQualityMetrics suggestsMe: beadarraySNP, lumi Package: beadarraySNP Version: 1.24.0 Depends: methods, Biobase (>= 2.5.5), quantsmooth Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy License: GPL-2 Title: Normalization and reporting of Illumina SNP bead arrays Description: Importing data from Illumina SNP experiments and performing copy number calculations and reports. biocViews: CopyNumberVariants, SNP, GeneticVariability, TwoChannel, Preprocessing, DataImport Author: Jan Oosting Maintainer: Jan Oosting MD5sum: c7d0df61bca38e8481900ed667323610 source.ver: src/contrib/beadarraySNP_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/beadarraySNP_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/beadarraySNP_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/beadarraySNP_1.24.0.tgz vignettes: vignettes/beadarraySNP/inst/doc/beadarraySNP.pdf vignetteTitles: beadarraySNP.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/beadarraySNP/inst/doc/beadarraySNP.R Package: BeadDataPackR Version: 1.10.0 License: GPL-2 Archs: i386, x64 Title: Compression of Illumina BeadArray data Description: Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform biocViews: Microarray Author: Mike Smith, Andy Lynch Maintainer: Mike Smith MD5sum: c169f4248ef377c7b88e33bf71e11d6f source.ver: src/contrib/BeadDataPackR_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BeadDataPackR_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BeadDataPackR_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BeadDataPackR_1.10.0.tgz vignettes: vignettes/BeadDataPackR/inst/doc/BeadDataPackR.pdf vignetteTitles: BeadDataPackR.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadDataPackR/inst/doc/BeadDataPackR.R importsMe: beadarray Package: betr Version: 1.14.0 Depends: R(>= 2.6.0) Imports: Biobase (>= 2.5.5), limma, mvtnorm, methods, stats Suggests: Biobase License: LGPL Title: Identify differentially expressed genes in microarray time-course data Description: The betr package implements the BETR (Bayesian Estimation of Temporal Regulation) algorithm to identify differentially expressed genes in microarray time-course data. biocViews: Microarray, Bioinformatics, DifferentialExpression, TimeCourse Author: Martin Aryee Maintainer: Martin Aryee MD5sum: ee23b3e5b50afc61927186efab3fd996 source.ver: src/contrib/betr_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/betr_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/betr_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/betr_1.14.0.tgz vignettes: vignettes/betr/inst/doc/betr.pdf vignetteTitles: BETR Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/betr/inst/doc/betr.R Package: bgafun Version: 1.20.0 Depends: made4, seqinr,ade4 License: Artistic-2.0 Title: BGAfun A method to identify specifity determining residues in protein families Description: A method to identify specifity determining residues in protein families using Between Group Analysis biocViews: Bioinformatics,Classification Author: Iain Wallace Maintainer: Iain Wallace MD5sum: 33fa63edfe9cc6968abbeeb3cfa1b6b3 source.ver: src/contrib/bgafun_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/bgafun_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/bgafun_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bgafun_1.20.0.tgz vignettes: vignettes/bgafun/inst/doc/bgafun.pdf vignetteTitles: bgafun.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bgafun/inst/doc/bgafun.R Package: BGmix Version: 1.18.0 Depends: R (>= 2.3.1), KernSmooth License: GPL-2 Title: Bayesian models for differential gene expression Description: Fully Bayesian mixture models for differential gene expression biocViews: Microarray, DifferentialExpression, MultipleComparisons Author: Alex Lewin, Natalia Bochkina Maintainer: Alex Lewin MD5sum: 621c968387e61c2d20628449f5340983 source.ver: src/contrib/BGmix_1.18.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BGmix_1.18.0.tgz vignettes: vignettes/BGmix/inst/doc/BGmix.pdf vignetteTitles: BGmix Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BGmix/inst/doc/BGmix.R Package: bgx Version: 1.22.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Suggests: affydata, hgu95av2cdf License: GPL-2 Archs: i386, x64 Title: Bayesian Gene eXpression Description: Bayesian integrated analysis of Affymetrix GeneChips biocViews: Microarray, DifferentialExpression Author: Ernest Turro, Graeme Ambler, Anne-Mette K Hein Maintainer: Ernest Turro MD5sum: 5ddc4b6823ddce958f9822247e483b77 source.ver: src/contrib/bgx_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/bgx_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/bgx_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bgx_1.22.0.tgz vignettes: vignettes/bgx/inst/doc/bgx.pdf vignetteTitles: HowTo BGX hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bgx/inst/doc/bgx.R Package: BHC Version: 1.10.0 License: GPL-3 Archs: i386, x64 Title: Bayesian Hierarchical Clustering Description: The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets. biocViews: Microarray, Clustering Author: Rich Savage, Emma Cooke, Robert Darkins, Yang Xu Maintainer: Rich Savage MD5sum: 1a3b218e444a7b8f94659ec70ecf72ee source.ver: src/contrib/BHC_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BHC_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BHC_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BHC_1.10.0.tgz vignettes: vignettes/BHC/inst/doc/bhc.pdf vignetteTitles: Bayesian Hierarchical Clustering hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BHC/inst/doc/bhc.R Package: BicARE Version: 1.16.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase License: GPL-2 Archs: i386, x64 Title: Biclustering Analysis and Results Exploration Description: Biclustering Analysis and Results Exploration biocViews: Microarray, Transcription, Bioinformatics, Clustering Author: Pierre Gestraud Maintainer: Pierre Gestraud URL: http://bioinfo.curie.fr MD5sum: fa6e0d850d00911fa955df05a29e9b6a source.ver: src/contrib/BicARE_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BicARE_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BicARE_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BicARE_1.16.0.tgz vignettes: vignettes/BicARE/inst/doc/BicARE.pdf vignetteTitles: BicARE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BicARE/inst/doc/BicARE.R Package: bigmemoryExtras Version: 1.0.0 Depends: R (>= 2.12), bigmemory (>= 4.3) Imports: bigmemory, methods, Biobase Suggests: RUnit, BiocGenerics (>= 0.1.0) OS_type: unix License: Artistic-2.0 Title: An extension of the bigmemory package with added safety, convenience, and a factor class. Description: This package defines a "BigMatrix" ReferenceClass which adds safety and convenience features to the filebacked.big.matrix class from the bigmemory package. BigMatrix protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also protects against accidental data modification with a filesystem-based permissions system. We provide utilities for using BigMatrix-derived classes as assayData matrices within the Biobase package's eSet family of classes. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a "BigMatrixFactor" class, a file-backed matrix with factor properties. biocViews: Infrastructure, DataRepresentation Author: Peter M. Haverty Maintainer: Peter M. Haverty MD5sum: 4fb351c4218f8240a6bd1aa0f8a42f93 source.ver: src/contrib/bigmemoryExtras_1.0.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bigmemoryExtras_1.0.0.tgz vignettes: vignettes/bigmemoryExtras/inst/doc/bigmemoryExtras.pdf vignetteTitles: bigmemoryExtras hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bigmemoryExtras/inst/doc/bigmemoryExtras.R importsMe: gCMAP Package: Biobase Version: 2.18.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils Imports: methods, BiocGenerics Suggests: tools, tkWidgets, ALL License: Artistic-2.0 Archs: i386, x64 Title: Biobase: Base functions for Bioconductor Description: Functions that are needed by many other packages or which replace R functions. biocViews: Infrastructure, Bioinformatics Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon Maintainer: Bioconductor Package Maintainer MD5sum: 257ffbd8d658368656a1b6778fa38268 source.ver: src/contrib/Biobase_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Biobase_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Biobase_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Biobase_2.18.0.tgz vignettes: vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf, vignettes/Biobase/inst/doc/Bioconductor.pdf, vignettes/Biobase/inst/doc/esApply.pdf, vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf, vignettes/Biobase/inst/doc/HowTo.pdf, vignettes/Biobase/inst/doc/Qviews.pdf vignetteTitles: Notes for eSet developers, Bioconductor Overview, esApply Introduction, An introduction to Biobase and ExpressionSets, Notes for writing introductory 'how to' documents, quick views of eSet instances hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Biobase/inst/doc/BiobaseDevelopment.R, vignettes/Biobase/inst/doc/Bioconductor.R, vignettes/Biobase/inst/doc/esApply.R, vignettes/Biobase/inst/doc/ExpressionSetIntroduction.R, vignettes/Biobase/inst/doc/HowTo.R, vignettes/Biobase/inst/doc/Qviews.R dependsOnMe: a4Base, a4Core, ACME, affy, affycomp, affyContam, affycoretools, affyPLM, affyQCReport, AGDEX, Agi4x44PreProcess, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, ArrayExpress, arrayMvout, ArrayTools, beadarray, beadarraySNP, bgx, BicARE, BiocCaseStudies, BioMVCClass, BioNet, birta, BrainStars, CAMERA, cancerclass, Category, categoryCompare, cellHTS, cellHTS2, CGHbase, CGHcall, CGHregions, charm, chroGPS, clippda, clusterStab, CMA, cn.farms, cn.mops, codelink, convert, copa, ddCt, DESeq, DEXSeq, DFP, DSS, dualKS, dyebias, easyRNASeq, EBarrays, EDASeq, eisa, ExiMiR, fabia, factDesign, fastseg, flowClust, flowCore, flowWorkspace, frma, gaga, GeneAnswers, GeneExpressionSignature, GeneMeta, geneRecommender, GeneRegionScan, GeneSelectMMD, GeneSelector, genoset, GEOquery, GOFunction, goProfiles, GOstats, 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PROMISE, puma, pvac, qpgraph, R453Plus1Toolbox, randPack, ReadqPCR, RGalaxy, Rmagpie, rMAT, rols, rqubic, rSFFreader, Rtreemix, safe, SAGx, ShortRead, simpleaffy, SLGI, SNPchip, spade, spkTools, splicegear, synapter, TEQC, tigre, timecourse, topGO, TSSi, twilight, VanillaICE, VariantAnnotation, virtualArray, XDE, xmapcore suggestsMe: annotate, betr, BiocCaseStudies, BiocGenerics, biocViews, BSgenome, Category, DART, farms, genefilter, genefu, geneplotter, GlobalAncova, globaltest, Heatplus, les, nem, OSAT, pkgDepTools, ROC, survcomp, tkWidgets, TypeInfo, vbmp, widgetTools Package: BiocCaseStudies Version: 1.20.0 Depends: tools, methods, utils, Biobase Suggests: affy (>= 1.17.3), affyPLM (>= 1.15.1), affyQCReport (>= 1.17.0), ALL (>= 1.4.3), annaffy (>= 1.11.1), annotate (>= 1.17.3), AnnotationDbi (>= 1.1.6), apComplex (>= 2.5.0), Biobase (>= 1.17.5), bioDist (>= 1.11.3), biocGraph (>= 1.1.1), biomaRt (>= 1.13.5), CCl4 (>= 1.0.6), CLL (>= 1.2.4), Category (>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert (>= 1.15.0), gcrma (>= 2.11.1), genefilter (>= 1.17.6), geneplotter (>= 1.17.2), GO.db (>= 2.0.2), GOstats (>= 2.5.0), graph (>= 1.17.4), GSEABase (>= 1.1.13), hgu133a.db (>= 2.0.2), hgu95av2.db, hgu95av2cdf (>= 2.0.0), hgu95av2probe (>= 2.0.0), hopach (>= 1.13.0), KEGG.db (>= 2.0.2), kohonen (>= 2.0.2), lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma (>= 2.13.1), MASS (>= 7.2-38), MLInterfaces (>= 1.13.17), multtest (>= 1.19.0), org.Hs.eg.db (>= 2.0.2), ppiStats (>= 1.5.4), randomForest (>= 4.5-20), RBGL (>= 1.15.6), RColorBrewer (>= 1.0-2), Rgraphviz (>= 1.17.11), vsn (>= 3.4.0), weaver (>= 1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11) License: Artistic-2.0 Title: BiocCaseStudies: Support for the Case Studies Monograph Description: Software and data to support the case studies. biocViews: Infrastructure, Bioinformatics Author: R. Gentleman, W. Huber, F. Hahne, M. Morgan, S. Falcon Maintainer: Bioconductor Package Maintainer MD5sum: a00e75c9713d324c6bfc0971eb1687c3 source.ver: src/contrib/BiocCaseStudies_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BiocCaseStudies_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BiocCaseStudies_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BiocCaseStudies_1.20.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BiocGenerics Version: 0.4.0 Depends: methods, graphics, stats Imports: methods, graphics, stats Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses, oligo, affyPLM, RUnit License: Artistic-2.0 Title: Generic functions for Bioconductor Description: S4 generic functions needed by many other Bioconductor packages. biocViews: Infrastructure Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer MD5sum: ae874c6b065d87ef8f0e16299070ab5a source.ver: src/contrib/BiocGenerics_0.4.0.tar.gz win.binary.ver: 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ChIPpeakAnno, chipseq, ChromHeatMap, cn.mops, codelink, crlmm, cummeRbund, EDASeq, eisa, fastseg, ffpe, flowCore, flowFP, flowMerge, flowQ, flowStats, frma, GenomicFeatures, GenomicRanges, GGBase, ggbio, GGtools, graph, GSEABase, GSVA, Gviz, HTSeqGenie, IRanges, LVSmiRNA, MEDIPS, methylumi, minfi, MinimumDistance, MiRaGE, MotifDb, MotIV, nucleR, oligo, oligoClasses, OrganismDbi, pcaMethods, PING, prada, R453Plus1Toolbox, RCytoscape, REDseq, Repitools, RGalaxy, Ringo, rMAT, Rsamtools, rsbml, rtracklayer, ShortRead, simpleaffy, SLGI, snpStats, Streamer, tigre, triform, TSSi, VariantAnnotation, VariantTools, XDE suggestsMe: bigmemoryExtras, BiocInstaller, CellNOptR, ChIPXpress, CNORfuzzy, DBChIP, gCMAP, GeneNetworkBuilder, GOstats, inSilicoMerging, motifStack, Rcade, Rgraphviz Package: biocGraph Version: 1.20.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 Title: Graph examples and use cases in Bioinformatics Description: This package provides examples and code that make use of the different graph related packages produced by Bioconductor. biocViews: NetworkVisualization, GraphsAndNetworks Author: Li Long , Robert Gentleman , Seth Falcon Florian Hahne Maintainer: Florian Hahne MD5sum: 460d406131cee79d0033129261f4aefb source.ver: src/contrib/biocGraph_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/biocGraph_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/biocGraph_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/biocGraph_1.20.0.tgz vignettes: vignettes/biocGraph/inst/doc/biocGraph.pdf, vignettes/biocGraph/inst/doc/layingOutPathways.pdf vignetteTitles: Examples of plotting graphs Using Rgraphviz, HOWTO layout pathways hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/biocGraph/inst/doc/biocGraph.R, vignettes/biocGraph/inst/doc/layingOutPathways.R suggestsMe: BiocCaseStudies Package: BiocInstaller Version: 1.8.3 Depends: R (>= 2.15.0) Suggests: RUnit, BiocGenerics License: Artistic-2.0 Title: Install/Update Bioconductor and CRAN Packages Description: Installs/updates Bioconductor and CRAN packages biocViews: Software Author: Dan Tenenbaum and Biocore Team Maintainer: Bioconductor Package Maintainer MD5sum: c19dedfa043497076ecad08f6a78415b source.ver: src/contrib/BiocInstaller_1.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/BiocInstaller_1.8.3.zip win64.binary.ver: bin/windows64/contrib/2.15/BiocInstaller_1.8.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BiocInstaller_1.8.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: affylmGUI importsMe: affy, gcrma, oligoClasses, webbioc suggestsMe: pkgDepTools Package: biocViews Version: 1.26.0 Depends: R (>= 2.4.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit Suggests: Biobase License: Artistic-2.0 Title: Categorized views of R package repositories Description: structures for vocabularies and narratives of views biocViews: Infrastructure Author: VJ Carey , BJ Harshfield , S Falcon Maintainer: Bioconductor Package Maintainer URL: http://www.bioconductor.org/packages/release/BiocViews.html MD5sum: 42a8ab74075ac7bd36360fea33ed8ce5 source.ver: src/contrib/biocViews_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/biocViews_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/biocViews_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/biocViews_1.26.0.tgz vignettes: vignettes/biocViews/inst/doc/createReposHtml.pdf, vignettes/biocViews/inst/doc/HOWTO-BCV.pdf vignetteTitles: biocViews-CreateRepositoryHTML, biocViews-HOWTO hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/biocViews/inst/doc/createReposHtml.R, vignettes/biocViews/inst/doc/HOWTO-BCV.R Package: bioDist Version: 1.30.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 Title: Different distance measures Description: A collection of software tools for calculating distance measures. biocViews: Bioinformatics Author: B. Ding, R. Gentleman and Vincent Carey Maintainer: Bioconductor Package Maintainer MD5sum: 87d77ba501dac6091f3c5e0e535c3abb source.ver: src/contrib/bioDist_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/bioDist_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/bioDist_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bioDist_1.30.0.tgz vignettes: vignettes/bioDist/inst/doc/bioDist.pdf vignetteTitles: bioDist Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bioDist/inst/doc/bioDist.R dependsOnMe: flowQ suggestsMe: BiocCaseStudies Package: biomaRt Version: 2.14.0 Depends: methods Imports: utils, XML, RCurl Suggests: annotate License: Artistic-2.0 Title: Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene) Description: In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining. biocViews: Annotation Author: Steffen Durinck , Wolfgang Huber Maintainer: Steffen Durinck MD5sum: b428114e02b5f8d34ff541e86c7b0fd5 source.ver: src/contrib/biomaRt_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/biomaRt_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/biomaRt_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/biomaRt_2.14.0.tgz vignettes: vignettes/biomaRt/inst/doc/biomaRt.pdf vignetteTitles: The biomaRt users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/biomaRt/inst/doc/biomaRt.R dependsOnMe: ChIPpeakAnno, domainsignatures, easyRNASeq, gene2pathway, genefu, GenomeGraphs, VegaMC importsMe: affycoretools, ArrayExpressHTS, ChIPpeakAnno, DEXSeq, GenomicFeatures, Gviz, HTSanalyzeR, IdMappingRetrieval, methyAnalysis, phenoTest, R453Plus1Toolbox, RNAither suggestsMe: BiocCaseStudies, GeneAnswers, GenomicFeatures, Genominator, isobar, maDB, MiRaGE, oneChannelGUI, Rcade, ShortRead, SIM Package: BioMVCClass Version: 1.26.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL Title: Model-View-Controller (MVC) Classes That Use Biobase Description: Creates classes used in model-view-controller (MVC) design biocViews: Visualization, Infrastructure, GraphsAndNetworks Author: Elizabeth Whalen Maintainer: Elizabeth Whalen MD5sum: 6ac6df752b6c8028af0c8d29bdbfa590 source.ver: src/contrib/BioMVCClass_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BioMVCClass_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BioMVCClass_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BioMVCClass_1.26.0.tgz vignettes: vignettes/BioMVCClass/inst/doc/BioMVCClass.pdf vignetteTitles: BioMVCClass hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioMVCClass/inst/doc/BioMVCClass.R Package: BioNet Version: 1.16.0 Depends: R (>= 2.10.0), Biobase, graph, RBGL Imports: igraph0, AnnotationDbi Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) Title: Routines for the functional analysis of biological networks Description: This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. biocViews: Microarray, DataImport, GraphsAndNetworks, NetworkAnalysis, NetworkEnrichment, GeneExpression, DifferentialExpression Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ MD5sum: be4610be34282c228c94733848cc1546 source.ver: src/contrib/BioNet_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BioNet_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BioNet_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BioNet_1.16.0.tgz vignettes: vignettes/BioNet/inst/doc/bum1.pdf, vignettes/BioNet/inst/doc/bum2.pdf, vignettes/BioNet/inst/doc/cytoscape.pdf, vignettes/BioNet/inst/doc/prec_recall_large.pdf, vignettes/BioNet/inst/doc/prec_recall_small.pdf, vignettes/BioNet/inst/doc/Tutorial-3dplot.pdf, vignettes/BioNet/inst/doc/Tutorial.pdf vignetteTitles: bum1.pdf, bum2.pdf, cytoscape.pdf, prec_recall_large.pdf, prec_recall_small.pdf, Tutorial-3dplot.pdf, BioNet Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioNet/inst/doc/Tutorial.R importsMe: HTSanalyzeR Package: BioSeqClass Version: 1.16.0 Depends: R (>= 2.10), scatterplot3d Imports: Biostrings, ipred, e1071, klaR, randomForest, class, tree, nnet, rpart, party, foreign, Biobase, utils, stats, grDevices Suggests: scatterplot3d License: LGPL (>= 2.0) Title: Classification for Biological Sequences Description: Extracting Features from Biological Sequences and Building Classification Model biocViews: Classification Author: Li Hong sysptm@gmail.com Maintainer: Li Hong MD5sum: df29825d9db5a7602a6055df62e99e37 source.ver: src/contrib/BioSeqClass_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BioSeqClass_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BioSeqClass_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BioSeqClass_1.16.0.tgz vignettes: vignettes/BioSeqClass/inst/doc/BioSeqClass.pdf, vignettes/BioSeqClass/inst/doc/cvFFSClassify0005.pdf, vignettes/BioSeqClass/inst/doc/FeatureSets16.pdf, vignettes/BioSeqClass/inst/doc/workflow.pdf vignetteTitles: Using the BioSeqClass Package, cvFFSClassify0005.pdf, FeatureSets16.pdf, workflow.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioSeqClass/inst/doc/BioSeqClass.R Package: Biostrings Version: 2.26.3 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>= 1.15.37) Imports: graphics, methods, stats, utils, BiocGenerics, IRanges LinkingTo: IRanges Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy, affydata (>= 1.11.5), RUnit Enhances: Rmpi License: Artistic-2.0 Archs: i386, x64 Title: String objects representing biological sequences, and matching algorithms Description: Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. biocViews: SequenceMatching, Genetics, Sequencing, Infrastructure, DataImport, DataRepresentation Author: H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy Maintainer: H. Pages MD5sum: 7c7c1eef1ccd2208fd54118422bc9d91 source.ver: src/contrib/Biostrings_2.26.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/Biostrings_2.26.3.zip win64.binary.ver: bin/windows64/contrib/2.15/Biostrings_2.26.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Biostrings_2.26.3.tgz vignettes: vignettes/Biostrings/inst/doc/Biostrings2Classes.pdf, vignettes/Biostrings/inst/doc/matchprobes.pdf, vignettes/Biostrings/inst/doc/MultipleAlignments.pdf, vignettes/Biostrings/inst/doc/PairwiseAlignments.pdf vignetteTitles: A short presentation of the basic classes defined in Biostrings 2, Handling probe sequence information, Multiple Alignments, Pairwise Sequence Alignments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Biostrings/inst/doc/Biostrings2Classes.R, vignettes/Biostrings/inst/doc/matchprobes.R, vignettes/Biostrings/inst/doc/MultipleAlignments.R, vignettes/Biostrings/inst/doc/PairwiseAlignments.R dependsOnMe: altcdfenvs, BRAIN, BSgenome, ChIPpeakAnno, ChIPsim, CorMut, DECIPHER, deepSNV, easyRNASeq, GeneRegionScan, genomes, iPAC, minfi, MotifDb, oneChannelGUI, PWMEnrich, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Rsamtools, rSFFreader, SCAN.UPC, seqbias, ShortRead, waveTiling importsMe: AffyCompatible, ArrayExpressHTS, BCRANK, BioSeqClass, biovizBase, charm, ChIPpeakAnno, ChIPseqR, ChIPsim, DECIPHER, gcrma, GeneRegionScan, GenomicFeatures, girafe, gmapR, Gviz, gwascat, HiTC, HTSeqGenie, MEDIPS, MEDME, methVisual, microRNA, motifRG, MotIV, oligo, oligoClasses, OTUbase, pdInfoBuilder, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Rolexa, Rsamtools, rSFFreader, rtracklayer, ShortRead, VariantAnnotation, VariantTools suggestsMe: annotate, CSAR, exomeCopy, GenomicFeatures, GenomicRanges, microRNA, MiRaGE, pcaGoPromoter, procoil Package: biovizBase Version: 1.6.2 Depends: R (>= 2.10), methods Imports: methods, stats, grDevices, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, IRanges, GenomicRanges, Biostrings, Rsamtools, GenomicFeatures Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer License: Artistic-2.0 Archs: i386, x64 Title: Basic graphic utilities for visualization of genomic data. Description: The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency. biocViews: Infrastructure, Visualization, Bioinformatics, Preprocessing Author: Tengfei Yin, Michael Lawrence, Dianne Cook Maintainer: Tengfei Yin MD5sum: 2747e9a13a58dcc36ee213ad76582f5d source.ver: src/contrib/biovizBase_1.6.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/biovizBase_1.6.2.zip win64.binary.ver: bin/windows64/contrib/2.15/biovizBase_1.6.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/biovizBase_1.6.2.tgz vignettes: vignettes/biovizBase/inst/doc/intro.pdf, vignettes/biovizBase/inst/doc/intro-shrinkageFun.pdf, vignettes/biovizBase/inst/doc/intro-shrink-single.pdf vignetteTitles: An Introduction to biovizBase, intro-shrinkageFun.pdf, intro-shrink-single.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/biovizBase/inst/doc/intro.R dependsOnMe: qrqc importsMe: Gviz, qrqc Package: birta Version: 1.2.0 Depends: limma, MASS, R(>= 2.10), Biobase, methods License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Inference of Regulation of Transcriptional Activity Description: Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. birta (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states. biocViews: Microarray, Sequencing, GeneExpression, Transcription, Bioinformatics, GraphsAndNetworks Author: Benedikt Zacher, Khalid Abnaof, Stephan Gade, Erfan Younesi, Achim Tresch, Holger Froehlich Maintainer: Benedikt Zacher MD5sum: 281f765d143412599f6ce32cad7b850c source.ver: src/contrib/birta_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/birta_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/birta_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/birta_1.2.0.tgz vignettes: vignettes/birta/inst/doc/birta.pdf vignetteTitles: Bayesian Inference of Regulation of Transcriptional Activity hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/birta/inst/doc/birta.R Package: BitSeq Version: 1.2.2 Depends: Rsamtools, zlibbioc Imports: IRanges LinkingTo: Rsamtools, zlibbioc License: Artistic-2.0 Archs: i386, x64 Title: Transcript expression inference and differential expression analysis for RNA-seq data Description: The BitSeq package is targeted for transcript expression analysis and differential expression analysis of RNA-seq data in two stage process. In the first stage it uses Bayesian inference methodology to infer expression of individual transcripts from individual RNA-seq experiments. The second stage of BitSeq embraces the differential expression analysis of transcript expression. Providing expression estimates from replicates of multiple conditions, Log-Normal model of the estimates is used for inferring the condition mean transcript expression and ranking the transcripts based on the likelihood of differential expression. biocViews: GeneExpression, DifferentialExpression, HighThroughputSequencing, RNAseq Author: Peter Glaus, Antti Honkela and Magnus Rattray Maintainer: Peter Glaus MD5sum: 85acf969f5f3ddded6caf5b393a7ea04 source.ver: src/contrib/BitSeq_1.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/BitSeq_1.2.2.zip win64.binary.ver: bin/windows64/contrib/2.15/BitSeq_1.2.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BitSeq_1.2.2.tgz vignettes: vignettes/BitSeq/inst/doc/BitSeq.pdf vignetteTitles: BitSeq User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/BitSeq/inst/doc/BitSeq.R Package: BRAIN Version: 1.4.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 Title: Baffling Recursive Algorithm for Isotope distributioN calculations Description: Package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm described in the paper by J. Claesen, P. Dittwald, T. Burzykowski and D. Valkenborg. biocViews: Bioinformatics, MassSpectrometry, Proteomics Author: Piotr Dittwald, with contributions of Dirk Valkenborg and Jurgen Claesen Maintainer: Piotr Dittwald MD5sum: 4f4331ff03c725f707ffd580eb37f3b5 source.ver: src/contrib/BRAIN_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BRAIN_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BRAIN_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BRAIN_1.4.0.tgz vignettes: vignettes/BRAIN/inst/doc/BRAIN-vignette.pdf vignetteTitles: BRAIN Usage hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BRAIN/inst/doc/BRAIN-vignette.R Package: BrainStars Version: 1.2.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 Title: query gene expression data and plots from BrainStars (B*) Description: This package can search and get gene expression data and plots from BrainStars (B*). BrainStars is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. biocViews: Microarray, OneChannel, DataImport Author: Itoshi NIKAIDO Maintainer: Itoshi NIKAIDO MD5sum: 1dce773fdd849fff860981889eeaac5c source.ver: src/contrib/BrainStars_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BrainStars_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BrainStars_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BrainStars_1.2.0.tgz vignettes: vignettes/BrainStars/inst/doc/BrainStars.pdf vignetteTitles: BrainStars hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BrainStars/inst/doc/BrainStars.R Package: bridge Version: 1.22.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Robust Inference for Differential Gene Expression Description: Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. biocViews: Microarray,OneChannel,TwoChannel,DifferentialExpression Author: Raphael Gottardo Maintainer: Raphael Gottardo MD5sum: 2ea6f721a75103edf6fccf623ff2be48 source.ver: src/contrib/bridge_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/bridge_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/bridge_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bridge_1.22.0.tgz vignettes: vignettes/bridge/inst/doc/bridge.pdf vignetteTitles: bridge Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bridge/inst/doc/bridge.R Package: BSgenome Version: 1.26.1 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>= 1.13.6), GenomicRanges (>= 1.7.5), Biostrings (>= 2.23.3) Suggests: RUnit, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11), SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase License: Artistic-2.0 Title: Infrastructure for Biostrings-based genome data packages Description: Infrastructure shared by all the Biostrings-based genome data packages biocViews: Genetics, Infrastructure, DataRepresentation, SequenceMatching, Annotation, SNP Author: Herve Pages Maintainer: H. Pages MD5sum: c46bfe6388f351c7ee7a034e63fd784d source.ver: src/contrib/BSgenome_1.26.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/BSgenome_1.26.1.zip win64.binary.ver: bin/windows64/contrib/2.15/BSgenome_1.26.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BSgenome_1.26.1.tgz vignettes: vignettes/BSgenome/inst/doc/BSgenomeForge.pdf, vignettes/BSgenome/inst/doc/GenomeSearching.pdf vignetteTitles: How to forge a BSgenome data package, Efficient genome searching with Biostrings and the BSgenome data packages hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BSgenome/inst/doc/BSgenomeForge.R, vignettes/BSgenome/inst/doc/GenomeSearching.R dependsOnMe: ChIPpeakAnno, chipseq, easyRNASeq, htSeqTools, MEDIPS, REDseq, rGADEM importsMe: charm, ChIPpeakAnno, chipseq, ggbio, girafe, Gviz, MEDIPS, PING, R453Plus1Toolbox, Repitools, rtracklayer, VariantAnnotation suggestsMe: Biostrings, biovizBase, GeneRegionScan, GenomicFeatures, GenomicRanges, MiRaGE, oneChannelGUI, Repitools, waveTiling Package: bsseq Version: 0.6.2 Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, parallel, matrixStats Imports: scales, stats, graphics, Biobase, locfit Suggests: RUnit, bsseqData License: Artistic-2.0 Title: Analyze, manage and store bisulfite sequencing data Description: Tools for analyzing and visualizing bisulfite sequencing data biocViews: DNAMethylation Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen MD5sum: b34a4cdf94079b0069fa6cf3805850bf source.ver: src/contrib/bsseq_0.6.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/bsseq_0.6.2.zip win64.binary.ver: bin/windows64/contrib/2.15/bsseq_0.6.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bsseq_0.6.2.tgz vignettes: vignettes/bsseq/inst/doc/bsseq_analysis.pdf, vignettes/bsseq/inst/doc/bsseq.pdf vignetteTitles: Analyzing WGBS with bsseq, The bsseq user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bsseq/inst/doc/bsseq_analysis.R, vignettes/bsseq/inst/doc/bsseq.R Package: BufferedMatrix Version: 1.22.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) Archs: i386, x64 Title: A matrix data storage object held in temporary files Description: A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data. biocViews: Infrastructure Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad MD5sum: 37d5814a67dbc7883e1bedb9e8c9acf2 source.ver: src/contrib/BufferedMatrix_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BufferedMatrix_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BufferedMatrix_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BufferedMatrix_1.22.0.tgz vignettes: vignettes/BufferedMatrix/inst/doc/BufferedMatrix.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture1.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture2.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture3.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture4.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture5.pdf vignetteTitles: BufferedMatrix: Introduction, BufferedMatrixPicture1.pdf, BufferedMatrixPicture2.pdf, BufferedMatrixPicture3.pdf, BufferedMatrixPicture4.pdf, BufferedMatrixPicture5.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BufferedMatrix/inst/doc/BufferedMatrix.R dependsOnMe: BufferedMatrixMethods Package: BufferedMatrixMethods Version: 1.22.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) Archs: i386, x64 Title: Microarray Data related methods that utlize BufferedMatrix objects Description: Microarray analysis methods that use BufferedMatrix objects biocViews: Infrastructure Author: B. M. Bolstad Maintainer: B. M. Bolstad URL: http://www.bmbolstad.com MD5sum: 48df2e667dd72e60cb7a7b5b241a8872 source.ver: src/contrib/BufferedMatrixMethods_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BufferedMatrixMethods_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BufferedMatrixMethods_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BufferedMatrixMethods_1.22.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BUS Version: 1.14.0 Depends: R (>= 2.3.0), minet Imports: stats License: GPL-3 Archs: i386, x64 Title: Gene network reconstruction Description: This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical). biocViews: Preprocessing Author: Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini Maintainer: Yuanhua Liu MD5sum: 3724c24dac70c36eb8bb58962c1ada02 source.ver: src/contrib/BUS_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BUS_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BUS_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BUS_1.14.0.tgz vignettes: vignettes/BUS/inst/doc/bus.pdf vignetteTitles: bus.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BUS/inst/doc/bus.R Package: CALIB Version: 1.24.0 Depends: R (>= 2.10), limma, methods Imports: limma, methods, graphics, stats, utils License: LGPL Archs: i386, x64 Title: Calibration model for estimating absolute expression levels from microarray data Description: This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes. biocViews: Microarray,TwoChannel,Preprocessing Author: Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal Maintainer: Hui Zhao MD5sum: b87a23e79e4473ada38d6748b65a2198 source.ver: src/contrib/CALIB_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CALIB_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CALIB_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CALIB_1.24.0.tgz vignettes: vignettes/CALIB/inst/doc/quickstart.pdf, vignettes/CALIB/inst/doc/readme.pdf vignetteTitles: CALIB Overview, readme.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CALIB/inst/doc/quickstart.R Package: CAMERA Version: 1.14.0 Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5), igraph Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit Enhances: Rmpi, snow License: GPL (>= 2) Archs: i386, x64 Title: Collection of annotation related methods for mass spectrometry data Description: Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments biocViews: MassSpectrometry Author: Carsten Kuhl, Ralf Tautenhahn, Steffen Neumann {ckuhl|sneumann}@ipb-halle.de, rtautenh@scripps.edu Maintainer: Carsten Kuhl URL: http://msbi.ipb-halle.de/msbi/CAMERA/ MD5sum: 865ace52149237e62cf6e69be3c1bd9f source.ver: src/contrib/CAMERA_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CAMERA_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CAMERA_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CAMERA_1.14.0.tgz vignettes: vignettes/CAMERA/inst/doc/CAMERA.pdf vignetteTitles: Molecule Identification with CAMERA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CAMERA/inst/doc/CAMERA.R Package: cancerclass Version: 1.2.1 Depends: R (>= 2.10.1), Biobase, binom, methods, stats Suggests: cancerdata License: GPL 3 Archs: i386, x64 Title: Development and validation of diagnostic tests from high-dimensional molecular data Description: The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements. biocViews: Cancer, Microarray, Classification, Visualization Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla MD5sum: dfcffaf3a88afd7f490d35af520863be source.ver: src/contrib/cancerclass_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/cancerclass_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/cancerclass_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cancerclass_1.2.1.tgz vignettes: vignettes/cancerclass/inst/doc/vignette_cancerclass.pdf vignetteTitles: Cancerclass: An R package for development and validation of diagnostic tests from high-dimensional molecular data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cancerclass/inst/doc/vignette_cancerclass.R Package: CancerMutationAnalysis Version: 1.2.1 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE Archs: i386, x64 Title: Cancer mutation analysis Description: This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and passenger genes (which are mutated in tumor samples, but have no role in tumorigenesis) and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison. biocViews: Genetics, Bioinformatics, Software Author: Giovanni Parmigiani, Simina M. Boca Maintainer: Simina M. Boca MD5sum: 9a6fa2e56afe3c989fac4391b9be1905 source.ver: src/contrib/CancerMutationAnalysis_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/CancerMutationAnalysis_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/CancerMutationAnalysis_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CancerMutationAnalysis_1.2.1.tgz vignettes: vignettes/CancerMutationAnalysis/inst/doc/CancerMutationAnalysis.pdf vignetteTitles: CancerMutationAnalysisTutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: Category Version: 2.24.0 Depends: BiocGenerics (>= 0.3.2), AnnotationDbi (>= 0.1.15), Biobase (>= 2.17.8), methods Imports: BiocGenerics, graph, methods, Biobase, AnnotationDbi, RBGL, GSEABase (>= 1.19.3), genefilter, annotate (>= 1.15.6), stats, utils Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, Matrix, KEGG.db, GO.db, SNPchip (>= 2.3.11), geneplotter, limma, lattice, graph, Biobase, genefilter, methods, RUnit, org.Sc.sgd.db, GOstats License: Artistic-2.0 Title: Category Analysis Description: A collection of tools for performing category analysis. biocViews: Annotation, GO, Pathways, GeneSetEnrichment Author: R. Gentleman with contributions from S. Falcon and D.Sarkar Maintainer: Bioconductor Package Maintainer MD5sum: a697c428c036065d7cb40f4636a47f15 source.ver: src/contrib/Category_2.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Category_2.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Category_2.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Category_2.24.0.tgz vignettes: vignettes/Category/inst/doc/Category.pdf, vignettes/Category/inst/doc/ChromBand.pdf vignetteTitles: Using Categories to Analyze Microarray Data, Using Chromosome Bands as Categories hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Category/inst/doc/Category.R, vignettes/Category/inst/doc/ChromBand.R dependsOnMe: categoryCompare, eisa, GOstats, PCpheno importsMe: categoryCompare, cellHTS2, gCMAP, GOstats, PCpheno, phenoTest, ppiStats suggestsMe: BiocCaseStudies, cellHTS, MmPalateMiRNA, qpgraph Package: categoryCompare Version: 1.2.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), AnnotationDbi (>= 0.1.15), Category (>= 2.23.4) Imports: BiocGenerics, Biobase, AnnotationDbi, hwriter, GSEABase, Category, GOstats, annotate, colorspace, graph, RCytoscape (>= 1.5.11) Suggests: methods, GSEABase, hwriter, colorspace, graph, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter License: GPL-2 Title: Meta-analysis of high-throughput experiments using feature annotations Description: Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested). biocViews: Bioinformatics, Annotation, GO, MultipleComparisons, Pathways, GeneExpression Author: Robert M. Flight Maintainer: Robert M. Flight SystemRequirements: Cytoscape (>= 2.8.0) (if used for visualization of results, heavily suggested), CytoscapeRPC plugin (>= 1.8) MD5sum: bf723461486857213fad9dba7f9ab213 source.ver: src/contrib/categoryCompare_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/categoryCompare_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/categoryCompare_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/categoryCompare_1.2.0.tgz vignettes: vignettes/categoryCompare/inst/doc/categoryCompare_vignette.pdf vignetteTitles: categoryCompare: High-throughput data meta-analysis using gene annotations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: cellGrowth Version: 1.2.0 Depends: R (>= 2.12.0), locfit (>= 1.5-4) Imports: lattice License: Artistic-2.0 Title: Fitting cell population growth models Description: This package provides functionalities for the fitting of cell population growth models on experimental OD curves. biocViews: CellBasedAssays, MicrotitrePlateAssay, DataImport, Visualization, TimeCourse Author: Julien Gagneur , Andreas Neudecker Maintainer: Julien Gagneur MD5sum: ff03edf6efd6338c16659cffd5252501 source.ver: src/contrib/cellGrowth_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cellGrowth_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cellGrowth_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cellGrowth_1.2.0.tgz vignettes: vignettes/cellGrowth/inst/doc/cellGrowth.pdf, vignettes/cellGrowth/inst/doc/cellGrowth-platePlotex.pdf, vignettes/cellGrowth/inst/doc/cellGrowth-plotex.pdf, vignettes/cellGrowth/inst/doc/cellGrowth-welldatex.pdf vignetteTitles: Overview of the cellGrowth package., cellGrowth-platePlotex.pdf, cellGrowth-plotex.pdf, cellGrowth-welldatex.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cellGrowth/inst/doc/cellGrowth.R Package: cellHTS Version: 1.28.0 Depends: R (>= 2.10), prada (>= 1.9.4), RColorBrewer, Biobase (>= 1.11.12), genefilter (>= 1.11.2) Suggests: Category, GO.db, vsn (>= 2.0.35) License: Artistic-2.0 Title: Analysis of cell-based screens Description: Analysis of cell-based RNA interference screens biocViews: CellBasedAssays, Visualization Author: Wolfgang Huber , Ligia Bras , Michael Boutros Maintainer: Ligia Bras URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber MD5sum: 9191b06d838f45b2f7a7582ed4d52a01 source.ver: src/contrib/cellHTS_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cellHTS_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cellHTS_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cellHTS_1.28.0.tgz vignettes: vignettes/cellHTS/inst/doc/cellhts.pdf, vignettes/cellHTS/inst/doc/twoChannels.pdf, vignettes/cellHTS/inst/doc/twoWay.pdf vignetteTitles: Main vignette: End-to-end analysis of cell-based screens, Supplement: multi-channel assays, Supplement: two-way assays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cellHTS/inst/doc/cellhts.R, vignettes/cellHTS/inst/doc/twoChannels.R, vignettes/cellHTS/inst/doc/twoWay.R suggestsMe: prada Package: cellHTS2 Version: 2.22.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: prada, GSEABase, Category, stats4 License: Artistic-2.0 Title: Analysis of cell-based screens - revised version of cellHTS Description: This package provides tools for the analysis of high-throughput assays that were performed in 384-well microtitre plate (or analogous) formats. The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries. See ?cellHTS2 for a brief introduction. biocViews: CellBasedAssays, Preprocessing, Visualization Author: Ligia Bras, Wolfgang Huber , Michael Boutros , Gregoire Pau , Florian Hahne Maintainer: Joseph Barry URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber MD5sum: 6c2b9145f32b99d94dfb1fa9b2a61eac source.ver: src/contrib/cellHTS2_2.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cellHTS2_2.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cellHTS2_2.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cellHTS2_2.22.0.tgz vignettes: vignettes/cellHTS2/inst/doc/cellhts2Complete.pdf, vignettes/cellHTS2/inst/doc/cellhts2.pdf, vignettes/cellHTS2/inst/doc/twoChannels.pdf, vignettes/cellHTS2/inst/doc/twoWay.pdf vignetteTitles: Main vignette (complete version): End-to-end analysis of cell-based screens, Main vignette: End-to-end analysis of cell-based screens, Supplement: multi-channel assays, Supplement: enhancer-suppressor screens hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cellHTS2/inst/doc/cellhts2Complete.R, vignettes/cellHTS2/inst/doc/cellhts2.R, vignettes/cellHTS2/inst/doc/twoChannels.R, vignettes/cellHTS2/inst/doc/twoWay.R dependsOnMe: coRNAi, imageHTS, staRank importsMe: HTSanalyzeR, RNAinteract Package: CellNOptR Version: 1.4.0 Depends: R (>= 2.15.0), RBGL, graph, methods Suggests: Rgraphviz,RUnit, BiocGenerics Enhances: Rgraphviz License: GPL-2 Archs: i386, x64 Title: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data. Description: This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network. biocViews: CellBasedAssays, CellBiology, Proteomics, Bioinformatics, TimeCourse Author: T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve Maintainer: T.Cokelaer SystemRequirements: Graphviz version >= 2.2 MD5sum: 26ba2da9ff545690d17d20a9e34732d5 source.ver: src/contrib/CellNOptR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CellNOptR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CellNOptR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CellNOptR_1.4.0.tgz vignettes: vignettes/CellNOptR/inst/doc/CellNOptR0_1flowchart.pdf, vignettes/CellNOptR/inst/doc/CellNOptR-vignette.pdf, vignettes/CellNOptR/inst/doc/Fig2.pdf, vignettes/CellNOptR/inst/doc/Fig3.pdf, vignettes/CellNOptR/inst/doc/Fig4.pdf, vignettes/CellNOptR/inst/doc/Fig6.pdf, vignettes/CellNOptR/inst/doc/Fig7.pdf vignetteTitles: CellNOptR0_1flowchart.pdf, Main vignette:Playing with networks using CellNOptR, Fig2.pdf, Fig3.pdf, Fig4.pdf, Fig6.pdf, Fig7.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CellNOptR/inst/doc/CellNOptR-vignette.R dependsOnMe: CNORdt, CNORfuzzy, CNORode Package: CGEN Version: 1.10.0 Depends: R (>= 2.10.1), survival, cluster Suggests: cluster License: GPL-2 + file LICENSE Archs: i386, x64 Title: An R package for analysis of case-control studies in genetic epidemiology Description: An R package for analysis of case-control studies in genetic epidemiology biocViews: SNP, MultipleComparisons, Clustering Author: Samsiddhi Bhattacharjee, Nilanjan Chatterjee and William Wheeler Maintainer: William Wheeler MD5sum: e5d164a4257c42dcb4ce2f4c60f6bfd0 source.ver: src/contrib/CGEN_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGEN_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGEN_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGEN_1.10.0.tgz vignettes: vignettes/CGEN/inst/doc/vignette.pdf vignetteTitles: CGEN Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/CGEN/inst/doc/vignette.R Package: CGHbase Version: 1.18.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL Title: CGHbase: Base functions and classes for arrayCGH data analysis. Description: Contains functions and classes that are needed by arrayCGH packages. biocViews: Infrastructure, Microarray, CopyNumberVariants Author: Sjoerd Vosse, Mark van de Wiel Maintainer: Mark van de Wiel MD5sum: 9972d4a6fa7c463ef612c7578e0c16f4 source.ver: src/contrib/CGHbase_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGHbase_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGHbase_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGHbase_1.18.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: CGHcall, CGHnormaliter, CGHregions, sigaR importsMe: CGHnormaliter Package: CGHcall Version: 2.18.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall License: GPL (http://www.gnu.org/copyleft/gpl.html) Title: Calling aberrations for array CGH tumor profiles. Description: Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. biocViews: Microarray,Preprocessing,Visualization Author: Mark van de Wiel, Sjoerd Vosse Maintainer: Mark van de Wiel MD5sum: c1b084a11dcd7e96e57bb1c4dd4e6daf source.ver: src/contrib/CGHcall_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGHcall_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGHcall_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGHcall_2.18.0.tgz vignettes: vignettes/CGHcall/inst/doc/CGHcall.pdf vignetteTitles: CGHcall hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CGHcall/inst/doc/CGHcall.R dependsOnMe: CGHnormaliter importsMe: CGHnormaliter Package: cghMCR Version: 1.16.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL Title: Find chromosome regions showing common gains/losses Description: This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples. biocViews: Microarray, CopyNumberVariants Author: J. Zhang and B. Feng Maintainer: J. Zhang MD5sum: 001090a495d9a23b28da26f551e241d8 source.ver: src/contrib/cghMCR_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cghMCR_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cghMCR_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cghMCR_1.16.0.tgz vignettes: vignettes/cghMCR/inst/doc/findMCR.pdf vignetteTitles: cghMCR findMCR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cghMCR/inst/doc/findMCR.R Package: CGHnormaliter Version: 1.12.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) Title: Normalization of array CGH data with imbalanced aberrations. Description: Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). biocViews: Microarray, Preprocessing Author: Bart P.P. van Houte, Thomas W. Binsl, Hannes Hettling Maintainer: Bart P.P. van Houte MD5sum: 7e6ce3071ac12bef80b2673ac5ff8a4a source.ver: src/contrib/CGHnormaliter_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGHnormaliter_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGHnormaliter_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGHnormaliter_1.12.0.tgz vignettes: vignettes/CGHnormaliter/inst/doc/CGHnormaliter-method.pdf, vignettes/CGHnormaliter/inst/doc/CGHnormaliter.pdf vignetteTitles: CGHnormaliter-method.pdf, CGHnormaliter hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CGHnormaliter/inst/doc/CGHnormaliter.R Package: CGHregions Version: 1.16.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase License: GPL (http://www.gnu.org/copyleft/gpl.html) Title: Dimension Reduction for Array CGH Data with Minimal Information Loss. Description: Dimension Reduction for Array CGH Data with Minimal Information Loss biocViews: Microarray,CopyNumberVariants,Visualization Author: Sjoerd Vosse & Mark van de Wiel Maintainer: Sjoerd Vosse MD5sum: 5fb7905ee95f84be91e8b7620b6335ca source.ver: src/contrib/CGHregions_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGHregions_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGHregions_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGHregions_1.16.0.tgz vignettes: vignettes/CGHregions/inst/doc/CGHregions.pdf vignetteTitles: CGHcall hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CGHregions/inst/doc/CGHregions.R suggestsMe: ADaCGH2 Package: charm Version: 2.4.0 Depends: R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter Imports: BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses(>= 1.17.39), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils, limma, parallel, sva(>= 3.1.2) Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor License: LGPL (>= 2) Title: Analysis of DNA methylation data from CHARM microarrays Description: This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools. biocViews: Microarray, Bioinformatics, DNAMethylation Author: Martin Aryee, Peter Murakami, Harris Jaffee, Rafael Irizarry Maintainer: Peter Murakami MD5sum: 971f31b934e20f8de1eafa14e9af7e7a source.ver: src/contrib/charm_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/charm_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/charm_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/charm_2.4.0.tgz vignettes: vignettes/charm/inst/doc/charm.pdf vignetteTitles: charm Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/charm/inst/doc/charm.R Package: ChemmineR Version: 2.10.9 Depends: R (>= 2.10.0), methods Imports: graphics, methods, stats, RCurl License: Artistic-2.0 Title: Cheminformatics of Drug-like Small Molecule Data Description: ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures. biocViews: MicrotitrePlateAssay, CellBasedAssays, Visualization, Infrastructure, DataImport, Clustering, Bioinformatics, Proteomics Author: Y. Eddie Cao, Tyler Backman, Yan Wang, Thomas Girke Maintainer: ChemmineR Team URL: http://manuals.bioinformatics.ucr.edu/home/chemminer MD5sum: 49b5886bc340b9a4096c9f13d4448d84 source.ver: src/contrib/ChemmineR_2.10.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChemmineR_2.10.9.zip win64.binary.ver: bin/windows64/contrib/2.15/ChemmineR_2.10.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChemmineR_2.10.9.tgz vignettes: vignettes/ChemmineR/inst/doc/ChemmineR.pdf vignetteTitles: gpls Tutorial hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChemmineR/inst/doc/ChemmineR.R dependsOnMe: fmcsR Package: ChIPpeakAnno Version: 2.6.1 Depends: R (>= 2.10), grid,VennDiagram, BiocGenerics (>= 0.1.0), biomaRt, multtest, IRanges, Biostrings, BSgenome, BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma Imports: gplots, BiocGenerics, biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db, limma, AnnotationDbi Suggests: reactome.db License: GPL (>= 2) Title: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges. Description: The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages biocViews: Annotation, ChIPseq, ChIPchip Author: Lihua Julie Zhu, Herve Pages, Claude Gazin, Nathan Lawson, Jianhong Ou, Simon Lin, David Lapointe and Michael Green Maintainer: Lihua Julie Zhu MD5sum: 9f0cfbc091f6aba61e9c32ea095464fd source.ver: src/contrib/ChIPpeakAnno_2.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChIPpeakAnno_2.6.1.zip win64.binary.ver: bin/windows64/contrib/2.15/ChIPpeakAnno_2.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChIPpeakAnno_2.6.1.tgz vignettes: vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf vignetteTitles: ChIPpeakAnno Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.R dependsOnMe: REDseq importsMe: FunciSNP, REDseq suggestsMe: oneChannelGUI Package: chipseq Version: 1.8.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.4), GenomicRanges (>= 1.7.7), BSgenome, ShortRead Imports: methods, BiocGenerics, IRanges, BSgenome, GenomicRanges, lattice, ShortRead, stats Suggests: GenomicFeatures, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene License: Artistic-2.0 Archs: i386, x64 Title: chipseq: A package for analyzing chipseq data Description: Tools for helping process short read data for chipseq experiments biocViews: ChIPseq Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao Maintainer: Bioconductor Package Maintainer MD5sum: af2ed54c45cef1b41b1a5113d5a000e1 source.ver: src/contrib/chipseq_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/chipseq_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/chipseq_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/chipseq_1.8.0.tgz vignettes: vignettes/chipseq/inst/doc/Workflow.pdf vignetteTitles: A Sample ChIP-Seq analysis workflow hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipseq/inst/doc/Workflow.R dependsOnMe: PING importsMe: HTSeqGenie suggestsMe: ggbio, oneChannelGUI Package: ChIPseqR Version: 1.12.0 Depends: R (>= 2.10.0), methods, BiocGenerics, ShortRead Imports: Biostrings, fBasics, GenomicRanges, graphics, grDevices, HilbertVis, IRanges, methods, ShortRead, stats, timsac, utils License: GPL (>= 2) Archs: i386, x64 Title: Identifying Protein Binding Sites in High-Throughput Sequencing Data Description: ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well. biocViews: ChIPseq, Bioinformatics, Infrastructure Author: Peter Humburg Maintainer: Peter Humburg MD5sum: ef90729990239b8000af74678aa5169a source.ver: src/contrib/ChIPseqR_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChIPseqR_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ChIPseqR_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChIPseqR_1.12.0.tgz vignettes: vignettes/ChIPseqR/inst/doc/Introduction.pdf vignetteTitles: Introduction to ChIPseqR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPseqR/inst/doc/Introduction.R Package: ChIPsim Version: 1.12.0 Depends: Biostrings Imports: IRanges, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) Title: Simulation of ChIP-seq experiments Description: A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. biocViews: Infrastructure, Bioinformatics, ChIPseq Author: Peter Humburg Maintainer: Peter Humburg MD5sum: c1806f8ec8f4521d6226711949a60c9f source.ver: src/contrib/ChIPsim_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChIPsim_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ChIPsim_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChIPsim_1.12.0.tgz vignettes: vignettes/ChIPsim/inst/doc/ChIPsimIntro.pdf vignetteTitles: Simulating ChIP-seq experiments hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPsim/inst/doc/ChIPsimIntro.R Package: ChIPXpress Version: 1.0.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL(>=2) Title: ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles Description: ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target. biocViews: ChIPchip, ChIPseq, Bioinformatics Author: George Wu Maintainer: George Wu MD5sum: 3d86cb2df0a01b67584959af1e82df01 source.ver: src/contrib/ChIPXpress_1.0.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChIPXpress_1.0.0.tgz vignettes: vignettes/ChIPXpress/inst/doc/ChIPXpress.pdf vignetteTitles: ChIPXpress hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPXpress/inst/doc/ChIPXpress.R Package: chopsticks Version: 1.22.4 Depends: R(>= 2.10.0), survival, methods Suggests: hexbin License: GPL-3 Archs: i386, x64 Title: The snp.matrix and X.snp.matrix classes Description: Implements classes and methods for large-scale SNP association studies biocViews: Microarray, SNPsAndGeneticVariability, SNP, GeneticVariability Author: Hin-Tak Leung Maintainer: Hin-Tak Leung URL: http://outmodedbonsai.sourceforge.net/ MD5sum: c7b45011bba7b071705a75e6b7df0ff2 source.ver: src/contrib/chopsticks_1.22.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/chopsticks_1.22.4.zip win64.binary.ver: bin/windows64/contrib/2.15/chopsticks_1.22.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/chopsticks_1.22.4.tgz vignettes: vignettes/chopsticks/inst/doc/chopsticks-vignette.pdf, vignettes/chopsticks/inst/doc/snpMatrix-4d.pdf, vignettes/chopsticks/inst/doc/snpMatrix-paper-HumanHeridity2007.pdf, vignettes/chopsticks/inst/doc/snpStatsBug_1.3.6_-vignette.pdf, vignettes/chopsticks/inst/doc/snpStatsBug_1.5.4_-vignette.pdf, vignettes/chopsticks/inst/doc/snpStatsBug-vignette.pdf vignetteTitles: snpMatrix, snpMatrix-4d.pdf, snpMatrix-paper-HumanHeridity2007.pdf, snpStatsBug_1.3.6_-vignette.pdf, snpStatsBug_1.5.4_-vignette.pdf, snpStatsBug-vignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chopsticks/inst/doc/chopsticks-vignette.R htmlDocs: vignettes/chopsticks/inst/doc/index.html Package: chroGPS Version: 1.0.1 Depends: R (>= 2.13.0), IRanges, methods, Biobase, MASS, graphics, stats, rgl Imports: graphics, cluster, DPpackage Enhances: multicore License: GPL (>=2) Title: chroGPS: navigating through the epigenome Description: We provide intuitive maps to visualize the association between genetic elements, with emphasis on epigenetics. The approach is based on Multi-Dimensional Scaling. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds. biocViews: Visualization, Clustering Author: Oscar Reina, David Rossell Maintainer: Oscar Reina MD5sum: b1414755970affa9fa03bed8a203a321 source.ver: src/contrib/chroGPS_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/chroGPS_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/chroGPS_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/chroGPS_1.0.1.tgz vignettes: vignettes/chroGPS/inst/doc/chroGPS.pdf vignetteTitles: Manual for the chroGPS library hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chroGPS/inst/doc/chroGPS.R Package: ChromHeatMap Version: 1.12.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0), hgu95av2.db Imports: BiocGenerics, annotate, AnnotationDbi, Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer Suggests: ALL License: Artistic-2.0 Title: Heat map plotting by genome coordinate Description: The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest. biocViews: Visualization Author: Tim F. Rayner Maintainer: Tim F. Rayner MD5sum: 29fef3a98dd9f1412dd5eaf03ab2a90c source.ver: src/contrib/ChromHeatMap_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChromHeatMap_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ChromHeatMap_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChromHeatMap_1.12.0.tgz vignettes: vignettes/ChromHeatMap/inst/doc/ChromHeatMap.pdf vignetteTitles: Plotting expression data with ChromHeatMap hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChromHeatMap/inst/doc/ChromHeatMap.R Package: clippda Version: 1.8.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>=2) Title: A package for the clinical proteomic profiling data analysis Description: Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations. biocViews: Proteomics, OneChannel, DataPreprocessing,Bioinformatics,DifferentialExpression, MultipleComparisons, SampleSize Author: Stephen Nyangoma Maintainer: Stephen Nyangoma URL: http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml MD5sum: 8b19e25e97b5f33e6ec737f5ff3021dc source.ver: src/contrib/clippda_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clippda_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clippda_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clippda_1.8.0.tgz vignettes: vignettes/clippda/inst/doc/clippda.pdf vignetteTitles: Sample Size Calculation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/clippda/inst/doc/clippda.R Package: Clonality Version: 1.6.0 Depends: R (>= 2.12.2), DNAcopy Imports: DNAcopy, grDevices, graphics, stats, utils Suggests: gdata, DNAcopy License: GPL-3 Title: Clonality testing Description: Statistical tests for clonality versus independence of tumors from the same patient based on their LOH or genomewide copy number profiles biocViews: Microarray, CopyNumberVariants, Classification, aCGH Author: Irina Ostrovnaya Maintainer: Irina Ostrovnaya MD5sum: 6e00c2bef18defc6e6f4954036c0da15 source.ver: src/contrib/Clonality_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Clonality_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Clonality_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Clonality_1.6.0.tgz vignettes: vignettes/Clonality/inst/doc/Clonality.pdf vignetteTitles: Clonality hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Clonality/inst/doc/Clonality.R Package: clst Version: 1.6.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 Title: Classification by local similarity threshold Description: Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons. biocViews: Classification Author: Noah Hoffman Maintainer: Noah Hoffman MD5sum: 41225bfa61056a46788efb2ff7fe7b8a source.ver: src/contrib/clst_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clst_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clst_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clst_1.6.0.tgz vignettes: vignettes/clst/inst/doc/clstDemo.pdf, vignettes/clst/inst/doc/matchtypes.pdf vignetteTitles: clst, matchtypes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/clst/inst/doc/clstDemo.R dependsOnMe: clstutils Package: clstutils Version: 1.6.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit, RSVGTipsDevice License: GPL-3 Title: Tools for performing taxonomic assignment. Description: Tools for performing taxonomic assignment based on phylogeny using pplacer and clst. biocViews: HighThroughputSequencing, Classification, Visualization, QualityControl Author: Noah Hoffman Maintainer: Noah Hoffman MD5sum: 1fa9524c5dcce06c63e6b693e423d742 source.ver: src/contrib/clstutils_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clstutils_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clstutils_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clstutils_1.6.0.tgz vignettes: vignettes/clstutils/inst/doc/pplacerDemo.pdf, vignettes/clstutils/inst/doc/refSet.pdf vignetteTitles: clst, clstutils hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/clstutils/inst/doc/pplacerDemo.R, vignettes/clstutils/inst/doc/refSet.R Package: clusterProfiler Version: 1.6.0 Depends: R (>= 2.10), ggplot2 Imports: methods, stats4, DBI, plyr, AnnotationDbi, GO.db, KEGG.db, org.Hs.eg.db, DOSE Suggests: GOSemSim, ReactomePA License: Artistic-2.0 Title: statistical analysis and visulization of functional profiles for genes and gene clusters Description: The package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters. biocViews: Clustering, GO, Pathways, Visualization, MultipleComparisons, GeneSetEnrichment Author: Guangchuang Yu, Li-Gen Wang Maintainer: Guangchuang Yu URL: http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118 MD5sum: c9dbd755ae774f353eccbac05192f6c0 source.ver: src/contrib/clusterProfiler_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clusterProfiler_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clusterProfiler_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clusterProfiler_1.6.0.tgz vignettes: vignettes/clusterProfiler/inst/doc/clusterProfiler_for_unsupported_organism.pdf, vignettes/clusterProfiler/inst/doc/clusterProfiler.pdf, vignettes/clusterProfiler/inst/doc/omics2012.pdf vignetteTitles: clusterProfiler_for_unsupported_organism.pdf, An introduction to clusterProfiler, omics2012.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/clusterProfiler/inst/doc/clusterProfiler.R suggestsMe: DOSE, GOSemSim, ReactomePA Package: clusterStab Version: 1.30.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 Title: Compute cluster stability scores for microarray data Description: This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters. biocViews: Clustering Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin Maintainer: James W. MacDonald MD5sum: 3106d9b02f81762848cbcb131ea3c3c4 source.ver: src/contrib/clusterStab_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clusterStab_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clusterStab_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clusterStab_1.30.0.tgz vignettes: vignettes/clusterStab/inst/doc/clusterStab.pdf vignetteTitles: clusterStab Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/clusterStab/inst/doc/clusterStab.R Package: CMA Version: 1.16.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st License: GPL (>= 2) Title: Synthesis of microarray-based classification Description: This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment. biocViews: Classification Author: Martin Slawski , Anne-Laure Boulesteix , Christoph Bernau . Maintainer: Christoph Bernau MD5sum: 45d104b02bc435b6a2e537b98dec84c2 source.ver: src/contrib/CMA_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CMA_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CMA_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CMA_1.16.0.tgz vignettes: vignettes/CMA/inst/doc/CMA_vignette.pdf vignetteTitles: CMA_vignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CMA/inst/doc/CMA_vignette.R Package: CNAnorm Version: 1.4.0 Depends: R (>= 2.10.1), DNAcopy, methods Imports: methods License: GPL-2 Archs: i386, x64 Title: A normalization method for Copy Number Aberration in cancer samples Description: Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found. biocViews: Bioinformatics, HighThroughputSequencing, CopyNumberVariants, Sequencing, Cancer, Lung Author: Stefano Berri , Henry M. Wood , Arief Gusnanto Maintainer: Stefano Berri URL: http://www.r-project.org, MD5sum: d6ec583d6b41b7a45c129e3702707a72 source.ver: src/contrib/CNAnorm_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNAnorm_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNAnorm_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNAnorm_1.4.0.tgz vignettes: vignettes/CNAnorm/inst/doc/CNAnorm.pdf vignetteTitles: CNAnorm.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: cn.farms Version: 1.6.0 Depends: R (>= 2.11), Biobase, methods, ff, oligoClasses, snowfall Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) Archs: i386, x64 Title: cn.farms - Factor Analysis for copy number estimation Description: This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff. biocViews: Microarray, Bioinformatics, CopyNumberVariants Author: Andreas Mitterecker, Djork-Arne Clevert Maintainer: Andreas Mitterecker URL: http://www.bioinf.jku.at/software/cnfarms/cnfarms.html MD5sum: 60e0aa032af25d1b63abe8c98a00aa3d source.ver: src/contrib/cn.farms_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cn.farms_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cn.farms_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cn.farms_1.6.0.tgz vignettes: vignettes/cn.farms/inst/doc/cn.farms.pdf vignetteTitles: cn.farms: Manual for the R package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cn.farms/inst/doc/cn.farms.R Package: cn.mops Version: 1.4.12 Depends: R (>= 2.12), BiocGenerics, Biobase, IRanges, GenomicRanges Imports: methods, graphics, BiocGenerics, IRanges, Rsamtools, Suggests: snow, DNAcopy License: LGPL (>= 2.0) Archs: i386, x64 Title: cn.mops - Mixture of Poissons for CNV detection in NGS data Description: cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++. biocViews: HighThroughputSequencing, Sequencing, Bioinformatics, CopyNumberVariants Author: Guenter Klambauer Maintainer: Guenter Klambauer URL: http://www.bioinf.jku.at/software/cnmops/cnmops.html MD5sum: 524aeda2384b608617a0397fea197d75 source.ver: src/contrib/cn.mops_1.4.12.tar.gz win.binary.ver: bin/windows/contrib/2.15/cn.mops_1.4.12.zip win64.binary.ver: bin/windows64/contrib/2.15/cn.mops_1.4.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cn.mops_1.4.12.tgz vignettes: vignettes/cn.mops/inst/doc/cn.mops.pdf vignetteTitles: cn.mops: Manual for the R package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cn.mops/inst/doc/cn.mops.R Package: CNORdt Version: 1.0.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 Archs: i386, x64 Title: Add-on to CellNOptR: Discretized time treatments Description: This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge. biocViews: CellBasedAssays, CellBiology, Proteomics, Bioinformatics, TimeCourse Author: A. MacNamara Maintainer: A. MacNamara MD5sum: 31d327e71e4ccf244ac3448d07a33625 source.ver: src/contrib/CNORdt_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNORdt_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNORdt_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNORdt_1.0.0.tgz vignettes: vignettes/CNORdt/inst/doc/CNORdt-vignette.pdf, vignettes/CNORdt/inst/doc/CNORdt-vignette-plot.pdf vignetteTitles: Using multiple time points to train logic models to data, CNORdt-vignette-plot.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CNORdt/inst/doc/CNORdt-vignette.R Package: CNORfuzzy Version: 1.0.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.3.29), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 Title: Addon to CellNOptR: Fuzzy Logic Description: This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL). Author: M. Morris, T. Cokelaer Maintainer: T. Cokelaer MD5sum: 8ecd008d76a6ed4ad3aa1dac8ec5056a source.ver: src/contrib/CNORfuzzy_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNORfuzzy_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNORfuzzy_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNORfuzzy_1.0.0.tgz vignettes: vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette-FullAnalysis2.pdf, vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette-FullAnalysis3.pdf, vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette-FullAnalysis.pdf, vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette.pdf, vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette-plotMeanFuzzyFit.pdf, vignettes/CNORfuzzy/inst/doc/tf1.pdf, vignettes/CNORfuzzy/inst/doc/tf2.pdf vignetteTitles: CNORfuzzy-vignette-FullAnalysis2.pdf, CNORfuzzy-vignette-FullAnalysis3.pdf, CNORfuzzy-vignette-FullAnalysis.pdf, Main vignette:Playing with networks using CNORfuzzyl, CNORfuzzy-vignette-plotMeanFuzzyFit.pdf, tf1.pdf, tf2.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette.R Package: CNORode Version: 1.0.0 Depends: CellNOptR, genalg Enhances: MEIGOR License: GPL-2 Archs: i386, x64 Title: ODE add-on to CellNOptR Description: ODE add-on to CellNOptR biocViews: CellBasedAssays, CellBiology, Proteomics, Bioinformatics, TimeCourse Author: David Henriques, Thomas Cokelaer Maintainer: David Henriques MD5sum: f496815811d2fe0f0048b8739eb7e9cf source.ver: src/contrib/CNORode_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNORode_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNORode_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNORode_1.0.0.tgz vignettes: vignettes/CNORode/inst/doc/CNORode-vignette.pdf, vignettes/CNORode/inst/doc/data_ToyModelMMB_FeddbackAnd.pdf vignetteTitles: Main vignette:Playing with networks using CNORode, data_ToyModelMMB_FeddbackAnd.pdf hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CNORode/inst/doc/CNORode-vignette.R Package: CNTools Version: 1.14.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL Archs: i386, x64 Title: Convert segment data into a region by sample matrix to allow for other high level computational analyses. Description: This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data biocViews: Microarray, CopyNumberVariants Author: Jianhua Zhang Maintainer: J. Zhang MD5sum: bca2952a88367a25c5a5d08dfb85818d source.ver: src/contrib/CNTools_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNTools_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNTools_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNTools_1.14.0.tgz vignettes: vignettes/CNTools/inst/doc/HowTo.pdf vignetteTitles: NCTools HowTo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CNTools/inst/doc/HowTo.R dependsOnMe: cghMCR Package: cnvGSA Version: 1.2.0 Depends: methods, brglm Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL Title: Gene Set Analysis of (Rare) Copy Number Variants Description: This package is intended to facilitate gene-set association with rare CNVs in case-control studies. biocViews: MultipleComparisons Author: Daniele Merico ; packaged by Robert Ziman Maintainer: Robert Ziman MD5sum: 10c5357dc56e6ff216424857b311e823 source.ver: src/contrib/cnvGSA_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cnvGSA_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cnvGSA_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cnvGSA_1.2.0.tgz vignettes: vignettes/cnvGSA/inst/doc/cnvGSA-vignette.pdf vignetteTitles: cnvGSA - Gene-Set Analysis of Rare Copy Number Variants hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cnvGSA/inst/doc/cnvGSA-vignette.R Package: CNVtools Version: 1.52.0 Depends: R (>= 2.10), survival License: GPL-3 Archs: i386, x64 Title: A package to test genetic association with CNV data Description: This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies. biocViews: GeneticVariability Author: Chris Barnes and Vincent Plagnol Maintainer: Chris Barnes MD5sum: 31608963d07c36455cbd9d79e919f58d source.ver: src/contrib/CNVtools_1.52.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNVtools_1.52.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNVtools_1.52.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNVtools_1.52.0.tgz vignettes: vignettes/CNVtools/inst/doc/CNVtools-vignette.pdf vignetteTitles: Copy Number Variation Tools hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CNVtools/inst/doc/CNVtools-vignette.R Package: CoCiteStats Version: 1.30.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL Title: Different test statistics based on co-citation. Description: A collection of software tools for dealing with co-citation data. biocViews: Bioinformatics Author: B. Ding and R. Gentleman Maintainer: Bioconductor Package Maintainer MD5sum: 57b65a69c56c5f19091a6f895768e40a source.ver: src/contrib/CoCiteStats_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CoCiteStats_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CoCiteStats_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CoCiteStats_1.30.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: codelink Version: 1.26.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: BiocGenerics, annotate Suggests: genefilter, parallel License: GPL-2 Title: Manipulation of Codelink Bioarrays data. Description: This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization. biocViews: Microarray, OneChannel, DataImport, Preprocessing Author: Diego Diez Maintainer: Diego Diez URL: http://www.kuicr.kyoto-u.ac.jp/~diez MD5sum: 34c1c8cfdd7d0360d55d558f5c6dda48 source.ver: src/contrib/codelink_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/codelink_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/codelink_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/codelink_1.26.0.tgz vignettes: vignettes/codelink/inst/doc/codelink.pdf, vignettes/codelink/inst/doc/CodelinkSet.pdf vignetteTitles: codelink, CodelinkSet hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/codelink/inst/doc/codelink.R, vignettes/codelink/inst/doc/CodelinkSet.R Package: CoGAPS Version: 1.8.0 Depends: R (>= 2.9.0), R.utils (>= 1.2.4), gplots (>= 2.8.0) Imports: graphics, grDevices, methods, stats, utils License: GPL (== 2) Title: Coordinated Gene Activity in Pattern Sets Description: Coordinated Gene Activity in Pattern Sets (CoGAPS) infers biological processes which are active in individual gene sets from corresponding microarray measurements. CoGAPS achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets. biocViews: GeneExpression, Microarray, Bioinformatics Author: Elana J. Fertig Maintainer: Elana J. Fertig , Michael F. Ochs URL: http://www.cancerbiostats.onc.jhmi.edu/CoGAPS.cfm SystemRequirements: GAPS-JAGS (==1.0.2) MD5sum: baaac5dfe7ffa17d703c17fb29261481 source.ver: src/contrib/CoGAPS_1.8.0.tar.gz vignettes: vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.pdf vignetteTitles: GAPS/CoGAPS Users Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.R Package: coGPS Version: 1.2.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 Title: cancer outlier Gene Profile Sets Description: Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies biocViews: Microarray, Bioinformatics, DifferentialExpression Author: Yingying Wei, Michael Ochs Maintainer: Yingying Wei MD5sum: c94137678c6074bd74724af1312ef431 source.ver: src/contrib/coGPS_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/coGPS_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/coGPS_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/coGPS_1.2.0.tgz vignettes: vignettes/coGPS/inst/doc/coGPS.pdf vignetteTitles: coGPS hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/coGPS/inst/doc/coGPS.R Package: ConsensusClusterPlus Version: 1.10.0 Imports: Biobase, ALL, graphics, stats, utils License: GPL version 2 Title: ConsensusClusterPlus Description: algorithm for determining cluster count and membership by stability evidence in unsupervised analysis biocViews: Software, Bioinformatics, Clustering Author: Matt Wilkerson Maintainer: Matt Wilkerson MD5sum: 67573d9ad4e5a4fed7cb600733dce724 source.ver: src/contrib/ConsensusClusterPlus_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ConsensusClusterPlus_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ConsensusClusterPlus_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ConsensusClusterPlus_1.10.0.tgz vignettes: vignettes/ConsensusClusterPlus/inst/doc/ConsensusClusterPlus.pdf vignetteTitles: ConsensusClusterPlus Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: convert Version: 1.34.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL Title: Convert Microarray Data Objects Description: Define coerce methods for microarray data objects. biocViews: Infrastructure, Microarray, TwoChannel Author: Gordon Smyth , James Wettenhall , Yee Hwa (Jean Yang) , Martin Morgan Martin Morgan Maintainer: Yee Hwa (Jean) Yang URL: http://bioinf.wehi.edu.au/limma/convert.html MD5sum: 842a69a470e5dfc3203670b3f7fbba6b source.ver: src/contrib/convert_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/convert_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/convert_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/convert_1.34.0.tgz vignettes: vignettes/convert/inst/doc/convert.pdf vignetteTitles: Converting Between Microarray Data Classes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/convert/inst/doc/convert.R htmlDocs: vignettes/convert/inst/doc/index.html dependsOnMe: maigesPack, TurboNorm suggestsMe: BiocCaseStudies, dyebias, OLIN Package: copa Version: 1.26.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 Archs: i386, x64 Title: Functions to perform cancer outlier profile analysis. Description: COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. biocViews: OneChannel, TwoChannel, DifferentialExpression, Visualization Author: James W. MacDonald Maintainer: James W. MacDonald MD5sum: 6dd60700c75cdc212007e6f00a0a6ac9 source.ver: src/contrib/copa_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/copa_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/copa_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/copa_1.26.0.tgz vignettes: vignettes/copa/inst/doc/copa.pdf vignetteTitles: copa Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/copa/inst/doc/copa.R Package: Cormotif Version: 1.4.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 Title: Correlation Motif Fit Description: It fits correlation motif model to multiple studies to detect study specific differential expression patterns. biocViews: Microarray, Bioinformatics, DifferentialExpression Author: Hongkai Ji, Yingying Wei Maintainer: Yingying Wei MD5sum: 4e82e6af2d3200a879714206a18c4a60 source.ver: src/contrib/Cormotif_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Cormotif_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Cormotif_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Cormotif_1.4.0.tgz vignettes: vignettes/Cormotif/inst/doc/CormotifVignette.pdf vignetteTitles: Cormotif Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Cormotif/inst/doc/CormotifVignette.R Package: CorMut Version: 1.0.0 Depends: methods, Biostrings, seqinr,igraph License: GPL-2 Title: Detect the correlated mutations based on selection pressure Description: CorMut provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Two methods are provided for detecting correlated mutations ,including conditional selection pressure and mutual information. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. biocViews: Bioinformatics, Sequencing Author: Zhenpeng Li, Yang Huang, Yabo Ouyang, Liying Ma Maintainer: Zhenpeng Li MD5sum: c5af394428e3f54a9b5f9c1da36c8d6b source.ver: src/contrib/CorMut_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CorMut_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CorMut_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CorMut_1.0.0.tgz vignettes: vignettes/CorMut/inst/doc/CorMut.pdf vignetteTitles: CorMut hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CorMut/inst/doc/CorMut.R Package: coRNAi Version: 1.8.0 Depends: R (>= 2.10), cellHTS2, limma, locfit Imports: MASS, gplots, lattice, grDevices, graphics, stats License: Artistic-2.0 Title: Analysis of co-knock-down RNAi data Description: Analysis of combinatorial cell-based RNAi screens biocViews: CellBasedAssays Author: Elin Axelsson Maintainer: Elin Axelsson SystemRequirements: Graphviz MD5sum: da4fcaf1487186a9113b8b9007133c1d source.ver: src/contrib/coRNAi_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/coRNAi_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/coRNAi_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/coRNAi_1.8.0.tgz vignettes: vignettes/coRNAi/inst/doc/coRNAi.pdf vignetteTitles: coRNAi hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/coRNAi/inst/doc/coRNAi.R Package: CORREP Version: 1.24.0 Imports: e1071, stats Suggests: cluster, MASS License: GPL (>= 2) Title: Multivariate Correlation Estimator and Statistical Inference Procedures. Description: Multivariate correlation estimation and statistical inference. See package vignette. biocViews: Bioinformatics, Microarray, Clustering, GraphsAndNetworks Author: Dongxiao Zhu and Youjuan Li Maintainer: Dongxiao Zhu MD5sum: c9ac04350fe6cb5dd4c8ac74a941bfb9 source.ver: src/contrib/CORREP_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CORREP_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CORREP_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CORREP_1.24.0.tgz vignettes: vignettes/CORREP/inst/doc/CORREP.pdf vignetteTitles: Multivariate Correlation Estimator hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CORREP/inst/doc/CORREP.R Package: cosmoGUI Version: 1.24.0 Depends: tkWidgets, cosmo License: LGPL (>= 2) Title: GUI for constructing constraint sets used by the cosmo package Description: cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch. biocViews: SequenceMatching, GUI Author: Fabian Gallusser, Oliver Bembom, and Sandrine Dudoit Maintainer: Oliver Bembom URL: http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/ucbbiostat/paper209/ MD5sum: 366138e121e89fcecb598c165dd2fff6 source.ver: src/contrib/cosmoGUI_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cosmoGUI_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cosmoGUI_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cosmoGUI_1.24.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cqn Version: 1.4.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 Title: Conditional quantile normalization Description: A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. biocViews: RNAseq, Preprocessing, DifferentialExpression Author: Jean (Zhijin) Wu, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen MD5sum: ccc60f56455b047d7232facac725ba4d source.ver: src/contrib/cqn_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cqn_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cqn_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cqn_1.4.0.tgz vignettes: vignettes/cqn/inst/doc/cqn.pdf vignetteTitles: CQN (Conditional Quantile Normalization) hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cqn/inst/doc/cqn.R importsMe: tweeDEseq Package: CRImage Version: 1.6.1 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 Title: CRImage a package to classify cells and calculate tumour cellularity Description: CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity. biocViews: CellBiology, Classification Author: Henrik Failmezger , Yinyin Yuan , Oscar Rueda , Florian Markowetz Maintainer: Henrik Failmezger , Yinyin Yuan MD5sum: 45ebbc5726f0f45311cdc7adbe822d44 source.ver: src/contrib/CRImage_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/CRImage_1.6.1.zip win64.binary.ver: bin/windows64/contrib/2.15/CRImage_1.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CRImage_1.6.1.tgz vignettes: vignettes/CRImage/inst/doc/cellularity2.pdf, vignettes/CRImage/inst/doc/CRImage.pdf, vignettes/CRImage/inst/doc/labeledImage.pdf, vignettes/CRImage/inst/doc/segmentedImage.pdf, vignettes/CRImage/inst/doc/segmentedImageRaw.pdf vignetteTitles: cellularity2.pdf, CRImage Manual, labeledImage.pdf, segmentedImage.pdf, segmentedImageRaw.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CRImage/inst/doc/CRImage.R Package: crlmm Version: 1.16.9 Depends: R (>= 2.14.0), oligoClasses (>= 1.19.39), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), ellipse, genefilter (>= 1.37.1), mvtnorm, splines, stats, SNPchip, utils, lattice, ff, foreach, RcppEigen LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.4), GGdata, snpStats, ellipse, RUnit License: Artistic-2.0 Archs: i386, x64 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms biocViews: Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry Maintainer: Benilton S Carvalho , Robert Scharpf , Matt Ritchie MD5sum: cf7411a6df6622feb7946461955dac5c source.ver: src/contrib/crlmm_1.16.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/crlmm_1.16.9.zip win64.binary.ver: bin/windows64/contrib/2.15/crlmm_1.16.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/crlmm_1.16.9.tgz vignettes: vignettes/crlmm/inst/doc/AffyGW.pdf, vignettes/crlmm/inst/doc/CopyNumberOverview.pdf, vignettes/crlmm/inst/doc/genotyping.pdf, vignettes/crlmm/inst/doc/gtypeDownstream.pdf, vignettes/crlmm/inst/doc/IlluminaPreprocessCN.pdf, vignettes/crlmm/inst/doc/Infrastructure.pdf vignetteTitles: Copy number estimation, Overview of copy number vignettes, crlmm Vignette - Genotyping, crlmm Vignette - Downstream Analysis, Preprocessing and genotyping Illumina arrays for copy number analysis, Infrastructure for copy number analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/crlmm/inst/doc/AffyGW.R, vignettes/crlmm/inst/doc/CopyNumberOverview.R, vignettes/crlmm/inst/doc/crlmmDownstream.R, vignettes/crlmm/inst/doc/genotyping.R, vignettes/crlmm/inst/doc/gtypeDownstream.R, vignettes/crlmm/inst/doc/IlluminaPreprocessCN.R, vignettes/crlmm/inst/doc/Infrastructure.R importsMe: minfi, VanillaICE suggestsMe: oligoClasses, SNPchip Package: CSAR Version: 1.10.0 Depends: R (>= 2.15.0), IRanges, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 Archs: i386, x64 Title: Statistical tools for the analysis of ChIP-seq data Description: Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation. biocViews: ChIPseq,Transcription,Genetics Author: Jose M Muino Maintainer: Jose M Muino MD5sum: 3cddb264f02bf01585ac1a7a49959fec source.ver: src/contrib/CSAR_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CSAR_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CSAR_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CSAR_1.10.0.tgz vignettes: vignettes/CSAR/inst/doc/CSAR.pdf vignetteTitles: CSAR Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CSAR/inst/doc/CSAR.R importsMe: NarrowPeaks suggestsMe: NarrowPeaks Package: ctc Version: 1.32.0 Depends: amap License: GPL-2 Title: Cluster and Tree Conversion. Description: Tools for export and import classification trees and clusters to other programs biocViews: Microarray, Clustering, Classification, DataImport, Visualization Author: Antoine Lucas , Laurent Gautier Maintainer: Antoine Lucas URL: http://antoinelucas.free.fr/ctc MD5sum: 004ec1bdf0c95016ce502ecbd020bd6a source.ver: src/contrib/ctc_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ctc_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ctc_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ctc_1.32.0.tgz vignettes: vignettes/ctc/inst/doc/ctc.pdf vignetteTitles: Introduction to ctc hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ctc/inst/doc/ctc.R Package: cummeRbund Version: 2.0.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics Suggests: cluster, plyr License: Artistic-2.0 Title: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. Description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. biocViews: HighThroughputSequencing, HighThroughputSequencingData, RNAseq, RNAseqData, GeneExpression, DifferentialExpression, Infrastructure, DataImport, DataRepresentation, Visualization, Bioinformatics, Clustering, MultipleComparisons, QualityControl Author: L. Goff, C. Trapnell, D. Kelley Maintainer: Loyal A. Goff MD5sum: b76bed64c322f27a706f627c2af8ee8c source.ver: src/contrib/cummeRbund_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cummeRbund_2.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cummeRbund_2.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cummeRbund_2.0.0.tgz vignettes: vignettes/cummeRbund/inst/doc/cuffData_schema.pdf, vignettes/cummeRbund/inst/doc/cummeRbund-example-workflow.pdf, vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf, vignettes/cummeRbund/inst/doc/ENCODE_SCV.pdf vignetteTitles: cuffData_schema.pdf, Sample cummeRbund workflow, CummeRbund User Guide, ENCODE_SCV.pdf hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cummeRbund/inst/doc/cummeRbund-example-workflow.R, vignettes/cummeRbund/inst/doc/cummeRbund-manual.R suggestsMe: oneChannelGUI Package: cycle Version: 1.12.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 Title: Significance of periodic expression pattern in time-series data Description: Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models biocViews: Microarray, Bioinformatics,TimeCourse Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/cycle/index.html MD5sum: cbcef5e4a02d260813f9f6120719ffb6 source.ver: src/contrib/cycle_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cycle_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cycle_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cycle_1.12.0.tgz vignettes: vignettes/cycle/inst/doc/cycle.pdf vignetteTitles: Introduction to cycle hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cycle/inst/doc/cycle.R Package: daMA Version: 1.30.0 Imports: MASS, stats License: GPL (>= 2) Title: Efficient design and analysis of factorial two-colour microarray data Description: This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted) biocViews: Microarray, TwoChannel, Bioinformatics, DifferentialExpression Author: Jobst Landgrebe and Frank Bretz Maintainer: Jobst Landgrebe URL: http://www.microarrays.med.uni-goettingen.de MD5sum: 79fb38ae5c4b737753dc7ee988e1ff19 source.ver: src/contrib/daMA_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/daMA_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/daMA_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/daMA_1.30.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DART Version: 1.4.0 Depends: R (>= 2.10.0), igraph0 Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 Title: Denoising Algorithm based on Relevance network Topology Description: Denoising Algorithm based on Relevance network Topology (DART) is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples. biocViews: GeneExpression, DifferentialExpression, GraphsAndNetworks, Pathways, Bioinformatics Author: Yan Jiao, Katherine Lawler, Andrew E Teschendorff Maintainer: Katherine Lawler MD5sum: 500d4317eef7c8afd5603a8a97ae788d source.ver: src/contrib/DART_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DART_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DART_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DART_1.4.0.tgz vignettes: vignettes/DART/inst/doc/DART.pdf vignetteTitles: DART Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DART/inst/doc/DART.R Package: DAVIDQuery Version: 1.18.0 Depends: RCurl (>= 1.4.0), utils License: GPL-2 Title: Retrieval from the DAVID bioinformatics data resource into R Description: Tools to retrieve data from DAVID, the Database for Annotation, Visualization and Integrated Discovery biocViews: Annotation Author: Roger Day, Alex Lisovich Maintainer: Roger Day MD5sum: 31f9af37515dd1afb3f481f7b6c3c8fa source.ver: src/contrib/DAVIDQuery_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DAVIDQuery_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DAVIDQuery_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DAVIDQuery_1.18.0.tgz vignettes: vignettes/DAVIDQuery/inst/doc/DAVIDQuery.pdf vignetteTitles: An R Package for retrieving data from DAVID into R objects. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DAVIDQuery/inst/doc/DAVIDQuery.R importsMe: IdMappingRetrieval Package: DBChIP Version: 1.2.0 Depends: R (>= 2.15.0), edgeR, DESeq Suggests: ShortRead, BiocGenerics License: GPL (>= 2) Title: Differential Binding of Transcription Factor with ChIP-seq Description: DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples. biocViews: ChIPseq, Sequencing, Transcription, Genetics, Bioinformatics Author: Kun Liang Maintainer: Kun Liang MD5sum: 2d0468c436fe43cb063118d6cd73fc89 source.ver: src/contrib/DBChIP_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DBChIP_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DBChIP_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DBChIP_1.2.0.tgz vignettes: vignettes/DBChIP/inst/doc/DBChIP.pdf vignetteTitles: DBChIP hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DBChIP/inst/doc/DBChIP.R Package: ddCt Version: 1.12.0 Depends: R (>= 2.3.0), Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, methods Suggests: RUnit License: LGPL-3 Title: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) Description: The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions. biocViews: GeneExpression, DifferentialExpression, MicrotitrePlateAssay, qPCR Author: Jitao David Zhang, Rudolf Biczok and Markus Ruschhaupt Maintainer: Jitao David Zhang MD5sum: 12682eac96a1e55c1e5151b060f1954a source.ver: src/contrib/ddCt_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ddCt_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ddCt_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ddCt_1.12.0.tgz vignettes: vignettes/ddCt/inst/doc/rtPCR.pdf, vignettes/ddCt/inst/doc/RT-PCR-Script-ddCt.pdf, vignettes/ddCt/inst/doc/rtPCR-usage.pdf vignetteTitles: Introduction to the ddCt method for qRT-PCR data analysis: background,, algorithm and example, How to apply the ddCt method, Analyse RT-PCR data with the end-to-end script in ddCt package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ddCt/inst/doc/rtPCR.R, vignettes/ddCt/inst/doc/RT-PCR-Script-ddCt.R, vignettes/ddCt/inst/doc/rtPCR-usage.R Package: ddgraph Version: 1.2.0 Depends: graph, methods, Rcpp Imports: bnlearn (>= 2.8), infotheo, gtools, pcalg, RColorBrewer, plotrix, MASS LinkingTo: Rcpp Suggests: testthat, Rgraphviz, e1071, ROCR, testthat License: GPL-3 Archs: i386, x64 Title: Distinguish direct and indirect interactions with Graphical Modelling Description: Distinguish direct from indirect interactions in gene regulation and infer combinatorial code from highly correlated variables such as transcription factor binding profiles. The package implements the Neighbourhood Consistent PC algorithm (NCPC) and draws Direct Dependence Graphs to represent dependence structure around a target variable. The package also provides a unified interface to other Graphical Modelling (Bayesian Network) packages for distinguishing direct and indirect interactions. biocViews: Bioinformatics, GraphsAndNetworks Author: Robert Stojnic Maintainer: Robert Stojnic MD5sum: aedc12ac6861d8f9f709f11abd0b4faf source.ver: src/contrib/ddgraph_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ddgraph_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ddgraph_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ddgraph_1.2.0.tgz vignettes: vignettes/ddgraph/inst/doc/ddgraph-cluster.pdf, vignettes/ddgraph/inst/doc/ddgraph-ddgraph-plot.pdf, vignettes/ddgraph/inst/doc/ddgraph.pdf vignetteTitles: ddgraph-cluster.pdf, ddgraph-ddgraph-plot.pdf, Overview of the 'ddgraph' package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ddgraph/inst/doc/ddgraph.R Package: DECIPHER Version: 1.4.0 Depends: R (>= 2.13.0), Biostrings (>= 2.16), RSQLite (>= 0.9), IRanges, stats Imports: Biostrings, RSQLite, IRanges, stats LinkingTo: Biostrings, RSQLite, IRanges, stats License: GPL-3 Archs: i386, x64 Title: Database Enabled Code for Ideal Probe Hybridization Employing R Description: A toolset that assist in the design of hybridization probes. biocViews: Clustering, Genetics, Sequencing, Infrastructure, DataImport, Visualization, Microarray, QualityControl Author: Erik Wright Maintainer: Erik Wright MD5sum: e9d35cd8dc7f1d4de36caa3029394242 source.ver: src/contrib/DECIPHER_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DECIPHER_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DECIPHER_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DECIPHER_1.4.0.tgz vignettes: vignettes/DECIPHER/inst/doc/DECIPHERing.pdf, vignettes/DECIPHER/inst/doc/DesignPrimers.pdf, vignettes/DECIPHER/inst/doc/FindChimeras.pdf vignetteTitles: Getting Started DECIPHERing, Design Group-Specific Primers, Finding Chimeric Sequences hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DECIPHER/inst/doc/DECIPHERing.R, vignettes/DECIPHER/inst/doc/DesignPrimers.R, vignettes/DECIPHER/inst/doc/FindChimeras.R Package: DeconRNASeq Version: 1.0.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 Title: Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data Description: DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles. biocViews: Bioinformatics, ExperimentData, RNAExpressionData Author: Ting Gong Joseph D. Szustakowski Maintainer: Ting Gong MD5sum: 09fc3e9c499b8788552bca497a82541b source.ver: src/contrib/DeconRNASeq_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DeconRNASeq_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DeconRNASeq_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DeconRNASeq_1.0.0.tgz vignettes: vignettes/DeconRNASeq/inst/doc/DeconRNASeq.pdf vignetteTitles: DeconRNASeq Demo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DeconRNASeq/inst/doc/DeconRNASeq.R Package: DEDS Version: 1.32.0 Depends: R (>= 1.7.0) License: LGPL Archs: i386, x64 Title: Differential Expression via Distance Summary for Microarray Data Description: This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach. biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Yuanyuan Xiao , Jean Yee Hwa Yang . Maintainer: Yuanyuan Xiao MD5sum: eac2b9851e6a73366a4726ce5142b6b0 source.ver: src/contrib/DEDS_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DEDS_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DEDS_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEDS_1.32.0.tgz vignettes: vignettes/DEDS/inst/doc/DEDS.pdf vignetteTitles: DEDS.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DEDS/inst/doc/DEDS.R Package: deepSNV Version: 1.4.0 Depends: R (>= 2.13.0), Rsamtools (>= 1.4.3), GenomicRanges, IRanges, Biostrings, VGAM, methods, graphics Imports: Rsamtools LinkingTo: Rsamtools License: GPL-3 Archs: i386, x64 Title: Detection of subclonal SNVs in deep sequencing experiments. Description: This package provides provides a quantitative variant caller for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. It assumes a comparative setup with a control experiment of the same loci and a beta-binomial model to discriminate sequencing errors and subclonal SNVs. biocViews: GeneticVariability, SNP, Sequencing, Genetics, DataImport Author: Moritz Gerstung and Niko Beerenwinkel Maintainer: Moritz Gerstung URL: http://www.cbg.ethz.ch/software/deepSNV MD5sum: 80582a5a973643b3f8584ddfd2bc5b99 source.ver: src/contrib/deepSNV_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/deepSNV_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/deepSNV_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/deepSNV_1.4.0.tgz vignettes: vignettes/deepSNV/inst/doc/deepSNV.pdf vignetteTitles: An R package for detecting low frequency variants in deep sequencing experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/deepSNV/inst/doc/deepSNV.R Package: DEGraph Version: 1.10.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 Title: Two-sample tests on a graph Description: DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results. biocViews: Microarray, DifferentialExpression, GraphsAndNetworks, NetworkAnalysis, NetworkEnrichment Author: Laurent Jacob, Pierre Neuvial and Sandrine Dudoit Maintainer: Laurent Jacob MD5sum: 6513411118526a0fdb65851025a3e060 source.ver: src/contrib/DEGraph_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DEGraph_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DEGraph_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEGraph_1.10.0.tgz vignettes: vignettes/DEGraph/inst/doc/DEGraph.pdf vignetteTitles: DEGraph: differential expression testing for gene networks hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DEGraph/inst/doc/DEGraph.R suggestsMe: graphite Package: DEGseq Version: 1.12.0 Depends: R (>= 2.8.0), qvalue, samr, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>=2) Archs: i386, x64 Title: Identify Differentially Expressed Genes from RNA-seq data Description: DEGseq is an R package to identify differentially expressed genes from RNA-Seq data. biocViews: RNAseq, Preprocessing, GeneExpression, DifferentialExpression Author: Likun Wang and Xi Wang . Maintainer: Likun Wang MD5sum: 718ffede5346e8e29b3efb2154db1dbc source.ver: src/contrib/DEGseq_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DEGseq_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DEGseq_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEGseq_1.12.0.tgz vignettes: vignettes/DEGseq/inst/doc/DEGseq.pdf vignetteTitles: DEGseq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DEGseq/inst/doc/DEGseq.R Package: DESeq Version: 1.10.1 Depends: Biobase (>= 2.13.11), locfit, lattice Imports: genefilter, geneplotter, methods, MASS, RColorBrewer Suggests: pasilla (>= 0.2.10), vsn, gplots License: GPL (>= 3) Archs: i386, x64 Title: Differential gene expression analysis based on the negative binomial distribution Description: Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution biocViews: HighThroughputSequencing, ChIPseq, RNAseq, SAGE, DifferentialExpression Author: Simon Anders, EMBL Heidelberg Maintainer: Simon Anders URL: http://www-huber.embl.de/users/anders/DESeq MD5sum: 1b95f6c724fd3609c22f112bb9864685 source.ver: src/contrib/DESeq_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/DESeq_1.10.1.zip win64.binary.ver: bin/windows64/contrib/2.15/DESeq_1.10.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DESeq_1.10.1.tgz vignettes: vignettes/DESeq/inst/doc/DESeq.pdf, vignettes/DESeq/inst/doc/vst.pdf vignetteTitles: Analysing RNA-Seq data with the "DESeq" package, vst.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DESeq/inst/doc/DESeq.R dependsOnMe: DBChIP, easyRNASeq, gCMAP importsMe: ArrayExpressHTS, DiffBind, EDASeq, rnaSeqMap suggestsMe: DiffBind, EDASeq, GenomicRanges, oneChannelGUI Package: DEXSeq Version: 1.4.0 Depends: Biobase (>= 2.13.11) Imports: biomaRt, hwriter, methods, stringr, statmod (>= 1.4.15) Suggests: pasilla (>= 0.2.13) Enhances: parallel License: GPL (>= 3) Title: Inference of differential exon usage in RNA-Seq Description: The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. biocViews: HighThroughputSequencing, RNAseq, DifferentialExpression Author: Simon Anders and Alejandro Reyes , both at EMBL Heidelberg Maintainer: Alejandro Reyes MD5sum: 0e679cf44416f27fb2718d74d3491afd source.ver: src/contrib/DEXSeq_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DEXSeq_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DEXSeq_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEXSeq_1.4.0.tgz vignettes: vignettes/DEXSeq/inst/doc/DEXSeq.pdf vignetteTitles: Analyzing RNA-seq data for differential exon usage with the "DEXSeq" package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DEXSeq/inst/doc/DEXSeq.R suggestsMe: GenomicRanges Package: DFP Version: 1.16.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 Title: Gene Selection Description: This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values. biocViews: Bioinformatics, Microarray, DifferentialExpression Author: R. Alvarez-Gonzalez, D. Glez-Pena, F. Diaz, F. Fdez-Riverola Maintainer: Rodrigo Alvarez-Glez MD5sum: 45319033c657ff3dff877cb15cfddc3c source.ver: src/contrib/DFP_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DFP_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DFP_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DFP_1.16.0.tgz vignettes: vignettes/DFP/inst/doc/DFP.pdf vignetteTitles: Howto: Discriminat Fuzzy Pattern hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DFP/inst/doc/DFP.R Package: DiffBind Version: 1.4.2 Depends: R (>= 2.14.0), GenomicRanges Imports: RColorBrewer, amap, edgeR (>= 2.3.58), gplots, DESeq, grDevices, stats, utils, IRanges, zlibbioc LinkingTo: Rsamtools Suggests: DESeq Enhances: rgl, parallel License: Artistic-2.0 Archs: i386, x64 Title: Differential Binding Analysis of ChIP-Seq peak data Description: Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. biocViews: Bioinformatics, HighThroughputSequencing, ChIPseq Author: Rory Stark, Gordon Brown Maintainer: Rory Stark MD5sum: 8f6a455a01d16cbfe3aea6196f685871 source.ver: src/contrib/DiffBind_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/DiffBind_1.4.2.zip win64.binary.ver: bin/windows64/contrib/2.15/DiffBind_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DiffBind_1.4.2.tgz vignettes: vignettes/DiffBind/inst/doc/DiffBind.pdf vignetteTitles: DiffBind User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DiffBind/inst/doc/DiffBind.R Package: diffGeneAnalysis Version: 1.40.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL Title: Performs differential gene expression Analysis Description: Analyze microarray data biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Choudary Jagarlamudi Maintainer: Choudary Jagarlamudi MD5sum: abfee77173137064a4e30768cb3604b7 source.ver: src/contrib/diffGeneAnalysis_1.40.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/diffGeneAnalysis_1.40.0.zip win64.binary.ver: bin/windows64/contrib/2.15/diffGeneAnalysis_1.40.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/diffGeneAnalysis_1.40.0.tgz vignettes: vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf vignetteTitles: Documentation on diffGeneAnalysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.R Package: DirichletMultinomial Version: 1.0.0 Depends: IRanges Imports: stats4, methods Suggests: lattice, parallel, MASS, RColorBrewer, xtable License: LGPL-3 Archs: i386, x64 Title: Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data Description: Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial. biocViews: HighThroughputSequencing, Clustering, Classification Author: Martin Morgan Maintainer: Martin Morgan SystemRequirements: gsl MD5sum: 6f35898c921260a6fce276e195a37f50 source.ver: src/contrib/DirichletMultinomial_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DirichletMultinomial_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DirichletMultinomial_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DirichletMultinomial_1.0.0.tgz vignettes: vignettes/DirichletMultinomial/inst/doc/DirichletMultinomial.pdf vignetteTitles: An introduction to DirichletMultinomial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: dks Version: 1.4.0 Depends: R (>= 2.8) Imports: cubature License: GPL Title: The double Kolmogorov-Smirnov package for evaluating multiple testing procedures. Description: The dks package consists of a set of diagnostic functions for multiple testing methods. The functions can be used to determine if the p-values produced by a multiple testing procedure are correct. These functions are designed to be applied to simulated data. The functions require the entire set of p-values from multiple simulated studies, so that the joint distribution can be evaluated. biocViews: Bioinformatics,MultipleComparisons,QualityControl Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek MD5sum: a21668c48848ef735e1fab9f8123b075 source.ver: src/contrib/dks_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/dks_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/dks_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dks_1.4.0.tgz vignettes: vignettes/dks/inst/doc/betas2.pdf, vignettes/dks/inst/doc/dks.pdf vignetteTitles: betas2.pdf, dksTutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dks/inst/doc/dks.R Package: DNAcopy Version: 1.32.0 License: GPL (>= 2) Archs: i386, x64 Title: DNA copy number data analysis Description: Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number biocViews: Microarray, CopyNumberVariants Author: Venkatraman E. Seshan, Adam Olshen Maintainer: Venkatraman E. Seshan MD5sum: 9a32e8724e519de210fa4325e203ffcc source.ver: src/contrib/DNAcopy_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DNAcopy_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DNAcopy_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DNAcopy_1.32.0.tgz vignettes: vignettes/DNAcopy/inst/doc/DNAcopy.pdf vignetteTitles: DNAcopy hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DNAcopy/inst/doc/DNAcopy.R dependsOnMe: CGHcall, cghMCR, Clonality, CNAnorm, CRImage, snapCGH importsMe: Clonality, cn.farms, GWASTools, MinimumDistance, Repitools, snapCGH suggestsMe: ADaCGH2, beadarraySNP, Clonality, cn.mops, fastseg, genoset, Repitools Package: domainsignatures Version: 1.18.0 Depends: R (>= 2.4.0), KEGG.db, prada, biomaRt, methods Imports: AnnotationDbi License: Artistic-2.0 Title: Geneset enrichment based on InterPro domain signatures Description: Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure. biocViews: Annotation, Pathways, GeneSetEnrichment Author: Florian Hahne, Tim Beissbarth Maintainer: Florian Hahne MD5sum: ccecdc26c4ca6d7f8a5cbdb9f9aae871 source.ver: src/contrib/domainsignatures_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/domainsignatures_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/domainsignatures_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/domainsignatures_1.18.0.tgz vignettes: vignettes/domainsignatures/inst/doc/domainenrichment.pdf vignetteTitles: Gene set enrichment using InterPro domain signatures hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/domainsignatures/inst/doc/domainenrichment.R Package: DOSE Version: 1.4.0 Depends: R (>= 2.10), ggplot2 Imports: methods, plyr, qvalue, stats4, AnnotationDbi, DO.db, org.Hs.eg.db, igraph, scales, reshape2, graphics, GOSemSim Suggests: clusterProfiler, ReactomePA License: Artistic-2.0 Title: Disease Ontology Semantic and Enrichment analysis Description: Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring DO semantic similarities, and hypergeometric test for enrichment analysis. biocViews: Bioinformatics, Annotation Author: Guangchuang Yu, Li-Gen Wang Maintainer: Guangchuang Yu MD5sum: ace5db23bd1a6102e801770b6c1800e4 source.ver: src/contrib/DOSE_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DOSE_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DOSE_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DOSE_1.4.0.tgz vignettes: vignettes/DOSE/inst/doc/DOSE.pdf vignetteTitles: An introduction to DOSE hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DOSE/inst/doc/DOSE.R dependsOnMe: ReactomePA importsMe: clusterProfiler suggestsMe: GOSemSim Package: DSS Version: 1.0.0 Depends: Biobase, locfdr Imports: methods License: GPL Title: Dispersion shrinakge for sequencing data. Description: DSS is an R library performing the differential expression analysis for RNA-seq count data. DSS implements a new dispersion shrinkage method to estimate the gene-specific biological variance. Extensive simulation results showed that DSS performs favorabily compared to DESeq and edgeR when the variation of biological variances is large. biocViews: HighThroughputSequencing, RNAseq, ChIPseq, DifferentialExpression Author: Hao Wu Maintainer: Hao Wu MD5sum: 3e87e45f73915ff3741f490c11113039 source.ver: src/contrib/DSS_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DSS_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DSS_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DSS_1.0.0.tgz vignettes: vignettes/DSS/inst/doc/DSS.pdf vignetteTitles: Differential expression for RNA-seq data with dispersion shrinkage hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DSS/inst/doc/DSS.R Package: DTA Version: 2.4.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 Title: Dynamic Transcriptome Analysis Description: Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements. biocViews: Microarray, DifferentialExpression, GeneExpression, Transcription Author: Bjoern Schwalb, Benedikt Zacher, Sebastian Duemcke, Achim Tresch Maintainer: Bjoern Schwalb MD5sum: a12915d55af318da52f11b8a9b8bc5f6 source.ver: src/contrib/DTA_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DTA_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DTA_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DTA_2.4.0.tgz vignettes: vignettes/DTA/inst/doc/DTA.pdf vignetteTitles: A guide to Dynamic Transcriptome Analysis (DTA) hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DTA/inst/doc/DTA.R Package: dualKS Version: 1.18.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.0), affy, methods License: LGPL (>= 2.0) Title: Dual KS Discriminant Analysis and Classification Description: This package implements a Kolmogorov Smirnov rank-sum based algorithm for training (i.e. discriminant analysis--identification of genes that discriminate between classes) and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes. biocViews: Microarray, Bioinformatics Author: Eric J. Kort, Yarong Yang Maintainer: Eric J. Kort MD5sum: ba95efef6f2ed7b3a34ddaa8dc8e7fc5 source.ver: src/contrib/dualKS_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/dualKS_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/dualKS_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dualKS_1.18.0.tgz vignettes: vignettes/dualKS/inst/doc/dualKS.pdf vignetteTitles: dualKS.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dualKS/inst/doc/dualKS.R Package: dyebias Version: 1.16.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 Title: The GASSCO method for correcting for slide-dependent gene-specific dye bias Description: Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21) biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad MD5sum: f4e809d85871d940726c24ed9dd1d593 source.ver: src/contrib/dyebias_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/dyebias_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/dyebias_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dyebias_1.16.0.tgz vignettes: vignettes/dyebias/inst/doc/dyebiasCompleteVignette.pdf, vignettes/dyebias/inst/doc/dyebias-vignette.pdf, vignettes/dyebias/inst/doc/gassco.pdf vignetteTitles: dyebiasCompleteVignette.pdf, dye bias correction, gassco.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/dyebias/inst/doc/dyebias-vignette.R Package: DynDoc Version: 1.36.0 Depends: methods, utils Imports: methods License: Artistic-2.0 Title: Dynamic document tools Description: A set of functions to create and interact with dynamic documents and vignettes. biocViews: ReportWriting, Infrastructure Author: R. Gentleman, Jeff Gentry Maintainer: Bioconductor Package Maintainer MD5sum: d4c647f134914d369e9587fb8d474f5a source.ver: src/contrib/DynDoc_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DynDoc_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DynDoc_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DynDoc_1.36.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: tkWidgets Package: EasyqpcR Version: 1.2.0 Imports: plyr, matrixStats, plotrix, gWidgetsRGtk2 Suggests: SLqPCR, qpcrNorm, qpcR, knitr License: GPL (>=2) Title: EasyqpcR for low-throughput real-time quantitative PCR data analysis Description: This package is based on the qBase algorithms published by Hellemans et al. in 2007. The EasyqpcR package allows you to import easily qPCR data files as described in the vignette. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors. This package has been created for low-throughput qPCR data analysis. biocViews: qPCR, GeneExpression Author: Le Pape Sylvain Maintainer: Le Pape Sylvain MD5sum: 23987219cbda1b3637681c763360a44f source.ver: src/contrib/EasyqpcR_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EasyqpcR_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EasyqpcR_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EasyqpcR_1.2.0.tgz vignettes: vignettes/EasyqpcR/inst/doc/vignette_EasyqpcR.pdf vignetteTitles: EasyqpcR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EasyqpcR/inst/doc/vignette_EasyqpcR.R Package: easyRNASeq Version: 1.4.2 Depends: graphics, methods, parallel, utils, genomeIntervals (>= 1.14.0), Biobase (>= 2.18.0), BiocGenerics (>= 0.4.0), biomaRt (>= 2.14.0), edgeR (>= 3.0.0), Biostrings (>= 2.26.0), BSgenome (>= 1.26.0), DESeq (>= 1.10.0), GenomicRanges (>= 1.10.0), IRanges (>= 1.16.0), Rsamtools (>= 1.10.0), ShortRead (>= 1.16.0) Suggests: BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), GenomicFeatures (>= 1.10.0), RnaSeqTutorial (>= 0.0.10) Enhances: edgeR, genomeIntervals, DESeq, ShortRead License: Artistic-2.0 Title: Count summarization and normalization for RNA-Seq data. Description: Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package. biocViews: GeneExpression, RNAseq, Genetics, Preprocessing Author: Nicolas Delhomme, Ismael Padioleau Maintainer: Nicolas Delhomme MD5sum: 3743cc970388ee7d03df3ae67f7bcb2b source.ver: src/contrib/easyRNASeq_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/easyRNASeq_1.4.2.zip win64.binary.ver: bin/windows64/contrib/2.15/easyRNASeq_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/easyRNASeq_1.4.2.tgz vignettes: vignettes/easyRNASeq/inst/doc/easyRNASeq.pdf vignetteTitles: RNA-Seq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/easyRNASeq/inst/doc/easyRNASeq.R Package: EBarrays Version: 2.22.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) Archs: i386, x64 Title: Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification Description: EBarrays provides tools for the analysis of replicated/unreplicated microarray data. biocViews: Clustering, DifferentialExpression Author: Ming Yuan, Michael Newton, Deepayan Sarkar and Christina Kendziorski Maintainer: Ming Yuan MD5sum: 7e79ce3957d58d26690c70dfc4ec6e8f source.ver: src/contrib/EBarrays_2.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EBarrays_2.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EBarrays_2.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EBarrays_2.22.0.tgz vignettes: vignettes/EBarrays/inst/doc/vignette.pdf vignetteTitles: Introduction to EBarrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EBarrays/inst/doc/vignette.R dependsOnMe: EBcoexpress, gaga suggestsMe: Category Package: EBcoexpress Version: 1.2.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) Archs: i386, x64 Title: EBcoexpress for Differential Co-Expression Analysis Description: An Empirical Bayesian Approach to Differential Co-Expression Analysis at the Gene-Pair Level Author: John A. Dawson Maintainer: John A. Dawson MD5sum: 383f4789003dd40458ca63ea0bca5250 source.ver: src/contrib/EBcoexpress_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EBcoexpress_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EBcoexpress_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EBcoexpress_1.2.0.tgz vignettes: vignettes/EBcoexpress/inst/doc/EBcoexpressVignette.pdf vignetteTitles: EBcoexpress Demo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EBcoexpress/inst/doc/EBcoexpressVignette.R Package: EBImage Version: 4.0.0 Imports: methods, graphics, stats, abind, utils, tiff, jpeg, png License: LGPL Archs: i386, x64 Title: Image processing toolbox for R Description: EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. biocViews: Visualization Author: Gregoire Pau, Andrzej Oles, Mike Smith, Oleg Sklyar, Wolfgang Huber Maintainer: Gregoire Pau MD5sum: b0724cf73201a893c3d575880b019b41 source.ver: src/contrib/EBImage_4.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EBImage_4.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EBImage_4.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EBImage_4.0.0.tgz vignettes: vignettes/EBImage/inst/doc/EBImage-introduction.pdf vignetteTitles: Introduction to EBImage hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EBImage/inst/doc/EBImage-installation.R, vignettes/EBImage/inst/doc/EBImage-introduction.R dependsOnMe: CRImage, imageHTS suggestsMe: HilbertVis Package: ecolitk Version: 1.30.1 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) Title: Meta-data and tools for E. coli Description: Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. biocViews: Annotation, Visualization Author: Laurent Gautier Maintainer: Laurent Gautier MD5sum: 1609b1cdcf2d60a02cc3962e1400f239 source.ver: src/contrib/ecolitk_1.30.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/ecolitk_1.30.1.zip win64.binary.ver: bin/windows64/contrib/2.15/ecolitk_1.30.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ecolitk_1.30.1.tgz vignettes: vignettes/ecolitk/inst/doc/ecolitk.pdf vignetteTitles: ecolitk hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ecolitk/inst/doc/ecolitk.R Package: EDASeq Version: 1.4.0 Depends: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), ShortRead (>= 1.11.42), Rsamtools (>= 1.5.75), aroma.light Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq Suggests: yeastRNASeq, leeBamViews, edgeR, DESeq License: Artistic-2.0 Title: Exploratory Data Analysis and Normalization for RNA-Seq Description: Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010). biocViews: HighThroughputSequencing, RNAseq, Preprocessing, QualityControl, DifferentialExpression Author: Davide Risso and Sandrine Dudoit Maintainer: Davide Risso MD5sum: 8adcf448b3a092bbad445afc104e57ed source.ver: src/contrib/EDASeq_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EDASeq_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EDASeq_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EDASeq_1.4.0.tgz vignettes: vignettes/EDASeq/inst/doc/EDASeq.pdf vignetteTitles: EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EDASeq/inst/doc/EDASeq.R suggestsMe: oneChannelGUI Package: edgeR Version: 3.0.8 Depends: R (>= 2.15.0), methods, limma Suggests: MASS, statmod, splines, locfit, KernSmooth License: GPL (>=2) Archs: i386, x64 Title: Empirical analysis of digital gene expression data in R Description: Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with other types of genome-scale count data. biocViews: Bioinformatics, DifferentialExpression, SAGE, HighThroughputSequencing, RNAseq, ChIPseq Author: Mark Robinson , Davis McCarthy , Yunshun Chen , Aaron Lun , Gordon Smyth Maintainer: Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth MD5sum: 838a554ee36938775df1c3ac5b4f3ce5 source.ver: src/contrib/edgeR_3.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/edgeR_3.0.8.zip win64.binary.ver: bin/windows64/contrib/2.15/edgeR_3.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/edgeR_3.0.8.tgz vignettes: vignettes/edgeR/inst/doc/edgeR.pdf, vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf vignetteTitles: edgeR Vignette, edgeRUsersGuide.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/edgeR/inst/doc/edgeR.R htmlDocs: vignettes/edgeR/inst/doc/index.html dependsOnMe: DBChIP, easyRNASeq, manta importsMe: ArrayExpressHTS, DiffBind, Repitools, rnaSeqMap, tweeDEseq suggestsMe: baySeq, cqn, EDASeq, GenomicRanges, goseq, GSVA, oneChannelGUI, Repitools Package: eisa Version: 1.10.0 Depends: BiocGenerics (>= 0.3.2), methods, isa2, Biobase (>= 2.17.8), AnnotationDbi, Category (>= 2.23.4), genefilter, DBI Imports: BiocGenerics Suggests: igraph0 (>= 0.5.5), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db License: GPL (>= 2) Title: Expression data analysis via the Iterative Signature Algorithm Description: The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. The ISA is capable of finding overlapping modules and it is resilient to noise. This package provides a convenient interface to the ISA, using standard BioConductor data structures; and also contains various visualization tools that can be used with other biclustering algorithms. biocViews: Classification, Visualization, Microarray, GeneExpression Author: Gabor Csardi Maintainer: Gabor Csardi MD5sum: 28f8871e24fa818c97c69713e8c97e53 source.ver: src/contrib/eisa_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/eisa_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/eisa_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/eisa_1.10.0.tgz vignettes: vignettes/eisa/inst/doc/EISA_biclust.pdf, vignettes/eisa/inst/doc/EISA_tutorial.pdf, vignettes/eisa/inst/doc/ISA_internals.pdf, vignettes/eisa/inst/doc/tissues.pdf vignetteTitles: The eisa and the biclust packages, The Iterative Signature Algorithm for Gene Expression Data, ISA_internals.pdf, tissues.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/eisa/inst/doc/EISA_biclust.R, vignettes/eisa/inst/doc/EISA_tutorial.R dependsOnMe: ExpressionView importsMe: ExpressionView Package: ENVISIONQuery Version: 1.6.0 Depends: rJava, XML, utils License: GPL-2 Title: Retrieval from the ENVISION bioinformatics data portal into R Description: Tools to retrieve data from ENVISION, the Database for Annotation, Visualization and Integrated Discovery portal biocViews: Annotation Author: Alex Lisovich, Roger Day Maintainer: Alex Lisovich , Roger Day MD5sum: 487d91db449cb0d260a350fb973c4750 source.ver: src/contrib/ENVISIONQuery_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ENVISIONQuery_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ENVISIONQuery_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ENVISIONQuery_1.6.0.tgz vignettes: vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.pdf vignetteTitles: An R Package for retrieving data from EnVision into R objects. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.R dependsOnMe: IdMappingRetrieval importsMe: IdMappingRetrieval Package: ExiMiR Version: 2.0.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) License: GPL-2 Title: R functions for the normalization of Exiqon miRNA array data Description: This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported. biocViews: Microarray, OneChannel, DualChannel, Preprocessing, GeneExpression, Transcription Author: Sylvain Gubian , Alain Sewer , PMP SA Maintainer: Sylvain Gubian MD5sum: b3c3530fdc67d3c8b66eb3bced24fbbc source.ver: src/contrib/ExiMiR_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ExiMiR_2.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ExiMiR_2.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ExiMiR_2.0.0.tgz vignettes: vignettes/ExiMiR/inst/doc/ExiMiR-vignette.pdf vignetteTitles: Description of ExiMiR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/ExiMiR/inst/doc/ExiMiR-vignette.R Package: exomeCopy Version: 1.4.4 Depends: IRanges, GenomicRanges, Rsamtools Imports: stats4, methods Suggests: Biostrings License: GPL (>= 2) Archs: i386, x64 Title: Copy number variant detection from exome sequencing read depth Description: Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count. biocViews: CopyNumberVariants, Sequencing, HighThroughputSequencing, Genetics Author: Michael Love Maintainer: Michael Love MD5sum: e75e1aa6a99e8b79c4378ccfe8b25c07 source.ver: src/contrib/exomeCopy_1.4.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/exomeCopy_1.4.4.zip win64.binary.ver: bin/windows64/contrib/2.15/exomeCopy_1.4.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/exomeCopy_1.4.4.tgz vignettes: vignettes/exomeCopy/inst/doc/exomeCopy.pdf vignetteTitles: Copy number variant detection in exome sequencing data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/exomeCopy/inst/doc/exomeCopy.R Package: explorase Version: 1.22.0 Depends: R (>= 2.6.2) Imports: limma, rggobi, RGtk2 Suggests: cairoDevice License: GPL-2 Title: GUI for exploratory data analysis of systems biology data Description: explore and analyze *omics data with R and GGobi biocViews: Visualization,Microarray,GUI Author: Michael Lawrence, Eun-kyung Lee, Dianne Cook, Jihong Kim, Hogeun An, and Dongshin Kim Maintainer: Michael Lawrence URL: http://www.metnetdb.org/MetNet_exploRase.htm MD5sum: 50ed0f32b753c3c46499c94342bd4c0f source.ver: src/contrib/explorase_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/explorase_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/explorase_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/explorase_1.22.0.tgz vignettes: vignettes/explorase/inst/doc/explorase.pdf vignetteTitles: Introduction to exploRase hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/explorase/inst/doc/explorase.R Package: ExpressionView Version: 1.10.1 Depends: caTools, bitops, methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Imports: methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Suggests: ALL, hgu95av2.db, biclust, affy License: GPL (>= 2) Archs: i386, x64 Title: Visualize biclusters identified in gene expression data Description: ExpressionView visualizes possibly overlapping biclusters in a gene expression matrix. It can use the result of the ISA method (eisa package) or the algorithms in the biclust package or others. The viewer itself was developed using Adobe Flex and runs in a flash-enabled web browser. biocViews: Classification, Visualization, Microarray, GeneExpression Author: Andreas Luscher Maintainer: Gabor Csardi MD5sum: 41bc71f53839f3d43b0d9b3191f3d819 source.ver: src/contrib/ExpressionView_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/ExpressionView_1.10.1.zip win64.binary.ver: bin/windows64/contrib/2.15/ExpressionView_1.10.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ExpressionView_1.10.1.tgz vignettes: vignettes/ExpressionView/inst/doc/ExpressionView.format.pdf, vignettes/ExpressionView/inst/doc/ExpressionView.ordering.pdf, vignettes/ExpressionView/inst/doc/ExpressionView.tutorial.pdf vignetteTitles: ExpressionView file format, How the ordering algorithm works, ExpressionView hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ExpressionView/inst/doc/ExpressionView.format.R, vignettes/ExpressionView/inst/doc/ExpressionView.ordering.R, vignettes/ExpressionView/inst/doc/ExpressionView.tutorial.R Package: externalVector Version: 1.24.0 Depends: R (>= 1.8.0), methods, stats License: LGPL Archs: i386, x64 Title: Vector objects for R with external storage Description: Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided. biocViews: Infrastructure Author: Saikat DebRoy Maintainer: Bioconductor Package Maintainer MD5sum: c277848030d8a38bf03c2362123e1507 source.ver: src/contrib/externalVector_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/externalVector_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/externalVector_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/externalVector_1.24.0.tgz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabia Version: 2.4.0 Depends: R (>= 2.8.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) Archs: i386, x64 Title: FABIA: Factor Analysis for Bicluster Acquisition Description: Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C. biocViews: Bioinformatics, Statistics, Microarray, DifferentialExpression, MultipleComparisons, Clustering, Visualization Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html MD5sum: 52f7d5c5ee4962ead582bfbfed0b5910 source.ver: src/contrib/fabia_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/fabia_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/fabia_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fabia_2.4.0.tgz vignettes: vignettes/fabia/inst/doc/fabia.pdf vignetteTitles: FABIA: Manual for the R package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fabia/inst/doc/fabia.R dependsOnMe: hapFabia Package: factDesign Version: 1.34.1 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL Title: Factorial designed microarray experiment analysis Description: This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Denise Scholtens Maintainer: Denise Scholtens MD5sum: cac052b9010f12c87b841c65651dc886 source.ver: src/contrib/factDesign_1.34.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/factDesign_1.34.1.zip win64.binary.ver: bin/windows64/contrib/2.15/factDesign_1.34.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/factDesign_1.34.1.tgz vignettes: vignettes/factDesign/inst/doc/factDesign.pdf vignetteTitles: factDesign hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/factDesign/inst/doc/factDesign.R Package: farms Version: 1.10.0 Depends: R (>= 2.8), affy (>= 1.20.0), MASS, methods Imports: affy, MASS, Biobase (>= 1.13.41), methods, graphics Suggests: affydata, Biobase, utils License: LGPL (>= 2.1) Title: FARMS - Factor Analysis for Robust Microarray Summarization Description: The package provides the summarization algorithm called Factor Analysis for Robust Microarray Summarization (FARMS) and a novel unsupervised feature selection criterion called "I/NI-calls" biocViews: GeneExpression, Microarray, Preprocessing, QualityControl Author: Djork-Arne Clevert Maintainer: Djork-Arne Clevert URL: http://www.bioinf.jku.at/software/farms/farms.html MD5sum: 07fcbfa81377110130883c5c7627cef2 source.ver: src/contrib/farms_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/farms_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/farms_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/farms_1.10.0.tgz vignettes: vignettes/farms/inst/doc/farms.pdf vignetteTitles: Using farms hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/farms/inst/doc/farms.R Package: fastseg Version: 1.4.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: graphics, stats, IRanges, BiocGenerics Suggests: DNAcopy, oligo License: LGPL (>= 2.0) Archs: i386, x64 Title: fastseg - a fast segmentation algorithm Description: fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments' first and higher order moments. biocViews: Classification, CopyNumberVariants Author: Guenter Klambauer Maintainer: Guenter Klambauer URL: http://www.bioinf.jku.at/software/fastseg/fastseg.html MD5sum: aef828c88395c4be14b1c6cdb050731a source.ver: src/contrib/fastseg_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/fastseg_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/fastseg_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fastseg_1.4.0.tgz vignettes: vignettes/fastseg/inst/doc/fastseg.pdf vignetteTitles: fastseg: Manual for the R package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fastseg/inst/doc/fastseg.R Package: fdrame Version: 1.30.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: FDR adjustments of Microarray Experiments (FDR-AME) Description: This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma biocViews: Microarray,DifferentialExpression,MultipleComparisons Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli Maintainer: Effi Kenigsberg MD5sum: 304bd77881502733851b72c7ba072e09 source.ver: src/contrib/fdrame_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/fdrame_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/fdrame_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fdrame_1.30.0.tgz vignettes: vignettes/fdrame/inst/doc/fdrame.pdf vignetteTitles: Annotation Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fdrame/inst/doc/fdrame.R Package: ffpe Version: 1.2.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, affy, ffpeExampleData License: GPL (>2) Title: Quality assessment and control for FFPE microarray expression data Description: Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots). biocViews: Microarray, GeneExpression, QualityControl, Bioinformatics Author: Levi Waldron Maintainer: Levi Waldron MD5sum: dd981105a231cd0b70f8d10ec4dbd65c source.ver: src/contrib/ffpe_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ffpe_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ffpe_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ffpe_1.2.0.tgz vignettes: vignettes/ffpe/inst/doc/ffpe.pdf vignetteTitles: ffpe package user guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ffpe/inst/doc/ffpe.R Package: flagme Version: 1.14.0 Depends: gcspikelite, xcms Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) Archs: i386, x64 Title: Analysis of Metabolomics GC/MS Data Description: Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data biocViews: Bioinformatics, DifferentialExpression, MassSpectrometry Author: Mark Robinson Maintainer: Mark Robinson MD5sum: 13cc0667f87c50bdf8be58d3274ed030 source.ver: src/contrib/flagme_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flagme_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flagme_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flagme_1.14.0.tgz vignettes: vignettes/flagme/inst/doc/flagme.pdf vignetteTitles: Using flagme -- Fragment-level analysis of GCMS-based metabolomics data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flagme/inst/doc/flagme.R Package: flowClust Version: 2.16.0 Depends: R(>= 2.5.0),BiocGenerics, methods, mnormt, ellipse, Biobase, flowCore(>= 1.11.23) Imports: stats4 Suggests: snowfall Enhances: multicore License: Artistic-2.0 Archs: i386, x64 Title: Clustering for Flow Cytometry Description: Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. biocViews: Clustering, Bioinformatics, Visualization, FlowCytometry Author: Raphael Gottardo , Kenneth Lo Maintainer: Raphael Gottardo MD5sum: 3e61455e37280bd874d4bc2568e7abc8 source.ver: src/contrib/flowClust_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowClust_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowClust_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowClust_2.16.0.tgz vignettes: vignettes/flowClust/inst/doc/flowClust.pdf vignetteTitles: flowClust package hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowClust/inst/doc/flowClust.R dependsOnMe: flowMerge importsMe: flowPhyto, flowTrans, flowType Package: flowCore Version: 1.24.2 Depends: R (>= 2.10.0), Biobase, rrcov Imports: Biobase, BiocGenerics (>= 0.1.14), feature, graph, graphics, grDevices, MASS, methods, rrcov, stats, utils, stats4 Suggests: Rgraphviz, flowViz, ncdf License: Artistic-2.0 Archs: i386, x64 Title: flowCore: Basic structures for flow cytometry data Description: Provides S4 data structures and basic functions to deal with flow cytometry data. biocViews: Infrastructure, FlowCytometry, CellBasedAssays Author: B. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan Maintainer: M.Jiang MD5sum: 37f283cb8da9763d96177f375d5c13c8 source.ver: src/contrib/flowCore_1.24.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowCore_1.24.2.zip win64.binary.ver: bin/windows64/contrib/2.15/flowCore_1.24.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowCore_1.24.2.tgz vignettes: vignettes/flowCore/inst/doc/HowTo-flowCore.pdf vignetteTitles: Basic Functions for Flow Cytometry Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowCore/inst/doc/HowTo-flowCore.R htmlDocs: vignettes/flowCore/inst/doc/fcs3.html dependsOnMe: flowFP, flowMerge, flowStats, flowTrans, flowUtils, flowViz, flowWorkspace, iFlow, ncdfFlow, plateCore importsMe: flowFlowJo, flowFP, flowMeans, flowPhyto, flowQ, flowStats, flowTrans, flowType, flowUtils, flowViz, flowWorkspace, iFlow, plateCore, spade suggestsMe: flowQB, RchyOptimyx Package: flowFlowJo Version: 1.16.0 Depends: R (>= 2.5.0), MASS, Imports: flowCore, XML (>= 1.96), methods, Biobase License: GPL (>=3) Title: Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm. Description: FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. biocViews: FlowCytometry Author: John J. Gosink Maintainer: John J. Gosink MD5sum: 6bef68fe8200c06cc5f57398ada53d36 source.ver: src/contrib/flowFlowJo_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowFlowJo_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowFlowJo_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowFlowJo_1.16.0.tgz vignettes: vignettes/flowFlowJo/inst/doc/flowFlowJo.pdf vignetteTitles: Basic Functions for working with FlowJo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowFlowJo/inst/doc/flowFlowJo.R Package: flowFP Version: 1.16.0 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), flowCore, flowViz, graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 Archs: i386, x64 Title: Fingerprinting for Flow Cytometry Description: Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. biocViews: Bioinformatics, FlowCytometry, CellBasedAssays, Clustering, Visualization Author: Herb Holyst , Wade Rogers Maintainer: Herb Holyst MD5sum: 399ff943d5d3602d1cc201930642fc22 source.ver: src/contrib/flowFP_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowFP_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowFP_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowFP_1.16.0.tgz vignettes: vignettes/flowFP/inst/doc/flowFP_HowTo.pdf vignetteTitles: Fingerprinting for Flow Cytometry hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowFP/inst/doc/flowFP_HowTo.R Package: flowMeans Version: 1.10.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 Title: Non-parametric Flow Cytometry Data Gating Description: Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required. biocViews: Bioinformatics, FlowCytometry, CellBiology, Clustering, Cancer, FlowCytData, StemCells, HIV Author: Nima Aghaeepour Maintainer: Nima Aghaeepour MD5sum: 0301d2eecb3e091545e9e739c450cfe0 source.ver: src/contrib/flowMeans_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowMeans_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowMeans_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowMeans_1.10.0.tgz vignettes: vignettes/flowMeans/inst/doc/flowMeans.pdf vignetteTitles: flowMeans: Non-parametric Flow Cytometry Data Gating hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowMeans/inst/doc/flowMeans.R importsMe: flowPhyto, flowType Package: flowMerge Version: 2.6.0 Depends: Rgraphviz, flowClust, flowCore, methods,snow,foreach,graph,feature Imports: rrcov, flowClust,flowCore, graphics, methods, rrcov, stats, utils, BiocGenerics (>= 0.1.6) Suggests: Rgraphviz Enhances: doMC, multicore License: Artistic-2.0 Title: Cluster Merging for Flow Cytometry Data Description: Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed. biocViews: Bioinformatics, Clustering, FlowCytometry Author: Greg Finak , Raphael Gottardo Maintainer: Greg Finak MD5sum: cf44b15180c5357663c5ef84f1c2c84f source.ver: src/contrib/flowMerge_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowMerge_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowMerge_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowMerge_2.6.0.tgz vignettes: vignettes/flowMerge/inst/doc/flowMerge.pdf vignetteTitles: flowMerge package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowMerge/inst/doc/flowMerge.R importsMe: flowType Package: flowPeaks Version: 1.0.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 Archs: i386, x64 Title: An R package for flow data clustering Description: A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means. biocViews: Flow cytometry, Clustering, Gating, Bioinformatics Author: Yongchao Ge Maintainer: Yongchao Ge MD5sum: 553b019842b10f0935363ab0a5e44103 source.ver: src/contrib/flowPeaks_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowPeaks_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowPeaks_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowPeaks_1.0.0.tgz vignettes: vignettes/flowPeaks/inst/doc/flowPeaks-guide.pdf vignetteTitles: Tutorial of flowPeaks package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowPeaks/inst/doc/flowPeaks-guide.R Package: flowPhyto Version: 1.10.0 Depends: R (>= 1.8.0) Imports: caroline, flowClust, flowCore, flowMeans, TTR Suggests: RPostgreSQL, zoo, maps, mapdata, plotrix License: Artistic-2.0 Title: Methods for Continuous Flow Cytometry Description: Automated Analysis of Continuous Flow Cytometry Data. biocViews: FlowCytometry, DataImport, QualityControl, Classification, Bioinformatics, Visualization, Clustering Author: Francois Ribalet and David M. Schruth Maintainer: David M. Schruth URL: http://seaflow.ocean.washington.edu MD5sum: b88ad09435b240148ee89da13be80207 source.ver: src/contrib/flowPhyto_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowPhyto_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowPhyto_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowPhyto_1.10.0.tgz vignettes: vignettes/flowPhyto/inst/doc/flowPhyto.pdf vignetteTitles: flowPhyto hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowPhyto/inst/doc/flowPhyto.R Package: flowPlots Version: 1.6.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 Title: flowPlots: analysis plots and data class for gated flow cytometry data Description: Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data. biocViews: FlowCytometry, CellBasedAssays, Visualization, DataRepresentation Author: N. Hawkins, S. Self Maintainer: N. Hawkins MD5sum: 6ad1ad117d0661c28483d652c484f21b source.ver: src/contrib/flowPlots_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowPlots_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowPlots_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowPlots_1.6.0.tgz vignettes: vignettes/flowPlots/inst/doc/flowPlots.pdf vignetteTitles: Plots with Embedded Tests for Gated Flow Cytometry Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowPlots/inst/doc/flowPlots.R Package: flowQ Version: 1.18.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.1.3), outliers, lattice, flowViz, mvoutlier, bioDist, parody, RColorBrewer, latticeExtra Imports: methods, BiocGenerics, geneplotter, flowCore, flowViz, IRanges Suggests: flowStats License: Artistic-2.0 Title: Quality control for flow cytometry Description: Provides quality control and quality assessment tools for flow cytometry data. biocViews: Infrastructure, FlowCytometry, CellBasedAssays Author: R. Gentleman, F. Hahne, J. Kettman, N. Le Meur, N. Gopalakrishnan Maintainer: Mike Jiang SystemRequirements: ImageMagick MD5sum: 98ecec21225c36367c4021672e0348ce source.ver: src/contrib/flowQ_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowQ_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowQ_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowQ_1.18.0.tgz vignettes: vignettes/flowQ/inst/doc/DataQualityAssessment.pdf, vignettes/flowQ/inst/doc/Extending-flowQ.pdf, vignettes/flowQ/inst/doc/flowQStructure.pdf, vignettes/flowQ/inst/doc/stainInfo.pdf vignetteTitles: Data Quality Assesment for Ungated Flow Cytometry Data, Basic Functions for Flow Cytometry Data, flowQStructure.pdf, stainInfo.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowQ/inst/doc/DataQualityAssessment.R, vignettes/flowQ/inst/doc/Extending-flowQ.R Package: flowQB Version: 1.0.1 Imports: Biobase, graphics,methods, flowCore,stats Suggests: flowCore License: Artistic-2.0 Title: Flow cytometer sensitivity-Automatic Q and B Calculations. Description: flowQB is a fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B), and electronic noise. biocViews: FlowCytometry Author: Faysal El Khettabi Maintainer: Faysal El Khettabi MD5sum: 7d323d793463d59bb1f83a634997a280 source.ver: src/contrib/flowQB_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowQB_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/flowQB_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowQB_1.0.1.tgz vignettes: vignettes/flowQB/inst/doc/flowQB_Sweave_.pdf vignetteTitles: flowQB package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowQB/inst/doc/flowQB_Sweave_.R Package: flowStats Version: 1.16.0 Depends: R (>= 2.10), flowCore (>= 1.10.0), fda (>= 2.2.6), mvoutlier, cluster, flowWorkspace Imports: BiocGenerics, MASS, flowViz, flowCore, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, utils, KernSmooth, lattice,compositions Suggests: flowViz, xtable Enhances: RBGL,ncdfFlow,graph License: Artistic-2.0 Title: Statistical methods for the analysis of flow cytometry data Description: Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package. biocViews: FlowCytometry, CellBasedAssays, Bioinformatics Author: Florian Hahne, Nishant Gopalakrishnan, Alireza Hadj Khodabakhshi, Chao-Jen Wong, Kyongryun Lee Maintainer: Greg Finak and Mike Jiang MD5sum: 707f4662ccc776f939b7389b7921e7f9 source.ver: src/contrib/flowStats_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowStats_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowStats_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowStats_1.16.0.tgz vignettes: vignettes/flowStats/inst/doc/GettingStartedWithFlowStats.pdf vignetteTitles: flowStats Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowStats/inst/doc/GettingStartedWithFlowStats.R dependsOnMe: iFlow importsMe: iFlow suggestsMe: flowQ Package: flowTrans Version: 1.10.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 Title: Parameter Optimization for Flow Cytometry Data Transformation Description: Profile maximum likelihood estimation of parameters for flow cytometry data transformations. biocViews: Bioinformatics, FlowCytometry Author: Greg Finak , Juan Manuel-Perez , Raphael Gottardo Maintainer: Greg Finak MD5sum: e74e8ea3ea961adf7234cc4536401b58 source.ver: src/contrib/flowTrans_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowTrans_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowTrans_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowTrans_1.10.0.tgz vignettes: vignettes/flowTrans/inst/doc/flowTrans.pdf vignetteTitles: flowTrans package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowTrans/inst/doc/flowTrans.R Package: flowType Version: 1.4.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, flowCore, flowMeans, sfsmisc, rrcov, flowClust, flowMerge, stats Suggests: xtable License: Artistic-2.0 Title: Phenotyping Flow Cytometry Assays Description: Phenotyping Flow Cytometry Assays using multidimentional expantion of single dimentional partitions. biocViews: FlowCytometry Author: Nima Aghaeepour Maintainer: Nima Aghaeepour MD5sum: 1b7178faf6514540b943ddb6af192489 source.ver: src/contrib/flowType_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowType_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowType_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowType_1.4.0.tgz vignettes: vignettes/flowType/inst/doc/flowType.pdf vignetteTitles: flowType package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowType/inst/doc/flowType.R suggestsMe: RchyOptimyx Package: flowUtils Version: 1.18.0 Depends: R (>= 2.2.0), flowCore (>= 1.2.0) Imports: Biobase, flowCore, graph, methods, RUnit, stats, utils, XML, flowViz Suggests: gatingMLData License: Artistic-2.0 Title: Utilities for flow cytometry Description: Provides utilities for flow cytometry data. biocViews: Infrastructure, FlowCytometry, CellBasedAssays Author: Gopalakrishnan N, F. Hahne, B. Ellis, R. Gentleman M. Dalphin,N. Le Meur, B. Purcell. Maintainer: Nishant Gopalakrishnan MD5sum: e4636950c739e63da1a3eef37d9bdd4c source.ver: src/contrib/flowUtils_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowUtils_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowUtils_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowUtils_1.18.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowViz Version: 1.22.0 Depends: R (>= 2.7.0), flowCore (>= 1.5.17), lattice, grDevices Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace,RColorBrewer License: Artistic-2.0 Title: Visualization for flow cytometry Description: Provides visualization tools for flow cytometry data. biocViews: Infrastructure, Flowcytometry, CellBasedAssays, Visualization Author: B. Ellis, R. Gentleman, F. Hahne, N. Le Meur, D. Sarkar Maintainer: Mike Jiang MD5sum: 71837a890d4f2c5b666a3df0d66ad91b source.ver: src/contrib/flowViz_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowViz_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowViz_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowViz_1.22.0.tgz vignettes: vignettes/flowViz/inst/doc/filters.pdf vignetteTitles: Visualizing Gates with Flow Cytometry Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowViz/inst/doc/filters.R dependsOnMe: flowFP, flowQ, flowWorkspace, iFlow, plateCore importsMe: flowFP, flowQ, flowStats, flowTrans, flowUtils, iFlow suggestsMe: flowCore, flowStats, spade Package: flowWorkspace Version: 1.4.0 Depends: Cairo, BiocGenerics, methods, RBGL, graph, XML, flowCore, flowViz, Biobase, IDPmisc, tools,hexbin Imports: Biobase, XML, flowCore, graph, graphics, lattice, methods, stats, stats4, utils Suggests: testthat, flowWorkspaceData, Rgraphviz Enhances: multicore,Rmpi,ncdfFlow License: Artistic-2.0 Archs: i386, x64 Title: Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore Description: This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis. biocViews: FlowCytometry, DataImport, Preprocessing, DataRepresentation Author: Greg Finak, Mike Jiang, Mose Andre Maintainer: Greg Finak MD5sum: 039ef031444868b8e18bf73d25fe5bea source.ver: src/contrib/flowWorkspace_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowWorkspace_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowWorkspace_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowWorkspace_1.4.0.tgz vignettes: vignettes/flowWorkspace/inst/doc/flowWorkspace.pdf vignetteTitles: Importing flowJo Workspaces into R hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowWorkspace/inst/doc/flowWorkspace.R dependsOnMe: flowStats Package: fmcsR Version: 1.0.5 Depends: R (>= 2.10.0), ChemmineR, methods License: Artistic-2.0 Archs: i386, x64 Title: Flexible Maximum Common Substructure (FMCS) Searching Description: The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering. biocViews: MicrotitrePlateAssay, CellBasedAssays, Visualization, Infrastructure, DataImport, Clustering, Bioinformatics, Proteomics Author: Yan Wang, Tyler Backman, Kevin Horan, Thomas Girke Maintainer: ChemmineR Team URL: http://manuals.bioinformatics.ucr.edu/home/chemminer MD5sum: ba6ac14864e38e37a6c59abe837e743b source.ver: src/contrib/fmcsR_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/fmcsR_1.0.5.zip win64.binary.ver: bin/windows64/contrib/2.15/fmcsR_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fmcsR_1.0.5.tgz vignettes: vignettes/fmcsR/inst/doc/fmcsR.pdf vignetteTitles: gpls Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fmcsR/inst/doc/fmcsR.R Package: frma Version: 1.10.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) Title: Frozen RMA and Barcode Description: Preprocessing and analysis for single microarrays and microarray batches. biocViews: Software, Microarray, Preprocessing Author: Matthew N. McCall , Rafael A. Irizarry , with contributions from Terry Therneau Maintainer: Matthew N. McCall URL: http://bioconductor.org MD5sum: 5ae0ea9031403c123749f3f44c55eef0 source.ver: src/contrib/frma_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/frma_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/frma_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/frma_1.10.0.tgz vignettes: vignettes/frma/inst/doc/frma.pdf vignetteTitles: frma: Preprocessing for single arrays and array batches hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/frma/inst/doc/frma.R importsMe: ChIPXpress suggestsMe: frmaTools Package: frmaTools Version: 1.10.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) Title: Frozen RMA Tools Description: Tools for advanced use of the frma package. biocViews: Software, Microarray, Preprocessing Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall URL: http://bioconductor.org MD5sum: 0908301a5cc39327145314bcae874038 source.ver: src/contrib/frmaTools_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/frmaTools_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/frmaTools_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/frmaTools_1.10.0.tgz vignettes: vignettes/frmaTools/inst/doc/frmaTools.pdf vignetteTitles: frmaTools: Create packages containing the vectors used by frma. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/frmaTools/inst/doc/frmaTools.R Package: FunciSNP Version: 1.1.8 Depends: R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data Imports: AnnotationDbi, IRanges, Rsamtools (>= 1.6.1), rtracklayer(>= 1.14.1), methods, ChIPpeakAnno (>= 2.2.0), GenomicRanges, VariantAnnotation, plyr, org.Hs.eg.db, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales Enhances: parallel License: GPL-3 Title: Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Description: FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions. biocViews: Infrastructure, DataRepresentation, DataImport, SequenceMatching, Annotation Author: Simon G. Coetzee and Houtan Noushmehr, PhD Maintainer: Simon G. Coetzee URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/ MD5sum: dfd00cd07d05ef6d23f44ae386bf2911 source.ver: src/contrib/FunciSNP_1.1.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/FunciSNP_1.1.8.zip win64.binary.ver: bin/windows64/contrib/2.15/FunciSNP_1.1.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/FunciSNP_1.1.8.tgz vignettes: vignettes/FunciSNP/inst/doc/FunciSNP_vignette.pdf, vignettes/FunciSNP/inst/doc/UCSC_genomeviewer_glioma.pdf vignetteTitles: FunciSNP Vignette, UCSC_genomeviewer_glioma.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FunciSNP/inst/doc/FunciSNP_vignette.R Package: gaga Version: 2.4.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: multicore License: GPL (>= 2) Archs: i386, x64 Title: GaGa hierarchical model for high-throughput data analysis Description: Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package). biocViews: OneChannel,MassSpectrometry,MultipleComparisons,DifferentialExpression,Classification Author: David Rossell . Maintainer: David Rossell MD5sum: 90769a9303bd3ab636261439b3550ea8 source.ver: src/contrib/gaga_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gaga_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gaga_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaga_2.4.0.tgz vignettes: vignettes/gaga/inst/doc/gagamanual.pdf vignetteTitles: Manual for the gaga library hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gaga/inst/doc/gagamanual.R Package: gage Version: 2.8.0 Depends: R (>= 2.10), graph, multtest Suggests: gageData, GO.db, GSEABase, KEGG.db, org.Hs.eg.db License: GPL (>=2.0) Title: Generally Applicable Gene-set Enrichment for Pathway Analysis Description: GAGE is a published method for gene set or pathway analysis. GAGE is generally applicable independent of microarray data attributes including sample sizes, experimental designs, microarray platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods. biocViews: Pathways, GO, DifferentialExpression, Microarray, OneChannel, TwoChannel, RNAseq, Genetics, MultipleComparisons, GeneSetEnrichment Author: Weijun Luo Maintainer: Weijun Luo URL: http://www.biomedcentral.com/1471-2105/10/161 MD5sum: ca598d0634c7351bf65763a00e108741 source.ver: src/contrib/gage_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gage_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gage_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gage_2.8.0.tgz vignettes: vignettes/gage/inst/doc/gage.pdf vignetteTitles: Generally Applicable Gene-set/Pathway Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gage/inst/doc/gage.R Package: gaggle Version: 1.26.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL version 2 or newer Title: Broadcast data between R and Gaggle Description: This package contains functions enabling data exchange between R and Gaggle enabled bioinformatics software, including Cytoscape, Firegoose and Gaggle Genome Browser. biocViews: ConnectTools, NetworkVisualization, Annotation, GraphsAndNetworks, DataImport Author: Paul Shannon Maintainer: Christopher Bare URL: http://gaggle.systemsbiology.net/docs/geese/r/ MD5sum: a8279a1307801fa331273d7d37795b57 source.ver: src/contrib/gaggle_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gaggle_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gaggle_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaggle_1.26.0.tgz vignettes: vignettes/gaggle/inst/doc/gaggle.pdf vignetteTitles: Gaggle Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gaggle/inst/doc/gaggle.R Package: gaia Version: 2.2.0 Depends: R (>= 2.10) License: GPL-2 Title: GAIA: An R package for genomic analysis of significant chromosomal aberrations. Description: This package allows to assess the statistical significance of chromosomal aberrations. biocViews: aCGH, CopyNumberVariants Author: Sandro Morganella et al. Maintainer: S. Morganella MD5sum: a7966f7a030357fcaacdac8714f859c9 source.ver: src/contrib/gaia_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gaia_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gaia_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaia_2.2.0.tgz vignettes: vignettes/gaia/inst/doc/gaia.pdf vignetteTitles: gaia hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gaia/inst/doc/gaia.R Package: gCMAP Version: 1.1.7 Depends: methods, GSEABase, DESeq Imports: Biobase, limma (>= 3.12.1), GSEAlm, Category, bigmemoryExtras (>= 0.99.3), Matrix (>= 1.0.9), parallel, annotate, genefilter, RColorBrewer, lattice, latticeExtra Suggests: KEGG.db, reactome.db, RUnit, BiocGenerics, reshape OS_type: unix License: Artistic-2.0 Title: Tools for Connectivity Map-like analyses Description: The gCMAP package provides a toolkit for comparing differential gene expression profiles through gene set enrichment analysis. Starting from normalized microarray or RNA-seq gene expression values (stored in lists of ExpressionSet and CountDataSet objects) the package performs differential expression analysis using the limma or DESeq packages. Supplying a simple list of gene identifiers, global differential expression profiles or data from complete experiments as input, users can use a unified set of several well-known gene set enrichment analysis methods to retrieve experiments with similar changes in gene expression. To take into account the directionality of gene expression changes, gCMAPQuery introduces the SignedGeneSet class, directly extending GeneSet from the GSEABase package. To increase performance of large queries, multiple gene sets are stored as sparse incidence matrices within CMAPCollection eSets. gCMAP offers implementations of 1. Fisher's exact test (Fisher, J R Stat Soc, 1922) 2. The "connectivity map" method (Lamb et al, Science, 2006) 3. Parametric and non-parametric t-statistic summaries (Jiang & Gentleman, Bioinformatics, 2007) and 4. Wilcoxon / Mann-Whitney rank sum statistics (Wilcoxon, Biometrics Bulletin, 1945) as well as wrappers for the 5. camera (Wu & Smyth, Nucleic Acid Res, 2012) 6. mroast and romer (Wu et al, Bioinformatics, 2010) functions from the limma package. All methods return CMAPResult objects, an S4 class inheriting from AnnotatedDataFrame, containing enrichment statistics as well as annotation data and providing simple high-level summary plots. biocViews: Bioinformatics, Microarray, Software, Pathways, Annotation Author: Thomas Sandmann , Richard Bourgon and Sarah Kummerfeld Maintainer: Thomas Sandmann MD5sum: 8c66e65e47e3ebe9fef671552273c4b0 source.ver: src/contrib/gCMAP_1.1.7.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gCMAP_1.1.7.tgz vignettes: vignettes/gCMAP/inst/doc/diffExprAnalysis.pdf, vignettes/gCMAP/inst/doc/gCMAP.pdf, vignettes/gCMAP/inst/doc/keggReactome.pdf vignetteTitles: main, main, main hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gCMAP/inst/doc/diffExprAnalysis.R, vignettes/gCMAP/inst/doc/gCMAP.R, vignettes/gCMAP/inst/doc/keggReactome.R Package: gcrma Version: 2.30.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), IRanges, Biostrings (>= 2.11.32), splines, BiocInstaller Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL Archs: i386, x64 Title: Background Adjustment Using Sequence Information Description: Background adjustment using sequence information biocViews: Microarray, OneChannel, Preprocessing Author: Jean(ZHIJIN) Wu, Rafael Irizarry with contributions from James MacDonald Jeff Gentry Maintainer: Z. Wu MD5sum: 13a24a8182b435d538fc0abb67e47ebd source.ver: src/contrib/gcrma_2.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gcrma_2.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gcrma_2.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gcrma_2.30.0.tgz vignettes: vignettes/gcrma/inst/doc/gcrma2.0.pdf vignetteTitles: gcrma1.2 hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gcrma/inst/doc/gcrma2.0.R dependsOnMe: affyILM, affyPLM, bgx, maskBAD, simpleaffy, webbioc importsMe: affycoretools, simpleaffy, virtualArray suggestsMe: AffyExpress, ArrayTools, BiocCaseStudies, panp Package: genArise Version: 1.34.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE Title: Microarray Analysis tool Description: genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. biocViews: Microarray, TwoChannel, Preprocessing Author: Ana Patricia Gomez Mayen ,\\ Gustavo Corral Guille , \\ Lina Riego Ruiz ,\\ Gerardo Coello Coutino Maintainer: IFC Development Team URL: http://www.ifc.unam.mx/genarise MD5sum: 8ca70f4c48247ecd1d2cc3bda26c754f source.ver: src/contrib/genArise_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genArise_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genArise_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genArise_1.34.0.tgz vignettes: vignettes/genArise/inst/doc/genArise.pdf vignetteTitles: genAriseGUI Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/genArise/inst/doc/genArise.R Package: gene2pathway Version: 2.12.0 Depends: R (>= 2.10.0), kernlab (>= 0.9), biomaRt (>= 1.12.1), KEGGSOAP (>= 1.12.0), RBGL, AnnotationDbi,org.Dm.eg.db, keggorthology (>= 2.0) Imports: SSOAP, RCurl Enhances: doMC License: GPL (>= 2) Title: Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures Description: The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained. biocViews: Microarray, Classification, GraphsAndNetworks, Pathways, NetworkEnrichment Author: Holger Froehlich Maintainer: Holger Froehlich MD5sum: 048520597a77d10c57a787b3038013cf source.ver: src/contrib/gene2pathway_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gene2pathway_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gene2pathway_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gene2pathway_2.12.0.tgz vignettes: vignettes/gene2pathway/inst/doc/gene2pathway.pdf vignetteTitles: gene2pathway hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gene2pathway/inst/doc/gene2pathway.R Package: GeneAnswers Version: 1.16.0 Depends: R (>= 2.10.0), igraph0, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, rgl, Heatplus, RColorBrewer Imports: graph, Rgraphviz, RBGL, annotate Suggests: GO.db, KEGG.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db License: LGPL (>= 2) Title: Integrated Interpretation of Genes Description: GeneAnswers provides an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test. biocViews: Infrastructure, DataRepresentation, Visualization, GraphsAndNetworks Author: Gang Feng, Pan Du, Tian Xia, Warren Kibbe and Simon Lin Maintainer: Gang Feng , Pan Du and Tian Xia MD5sum: a8b1a4bed91ee1a476fe47b1b3f04281 source.ver: src/contrib/GeneAnswers_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneAnswers_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneAnswers_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneAnswers_1.16.0.tgz vignettes: vignettes/GeneAnswers/inst/doc/GeneAnswersCWAnnotation.pdf, vignettes/GeneAnswers/inst/doc/geneAnswers.pdf, vignettes/GeneAnswers/inst/doc/geneFunctionSummarize.pdf vignetteTitles: GeneAnswers web-based visualization module, GeneAnswers, Summarize gene annotations based on collective ontology annotations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneAnswers/inst/doc/GeneAnswersCWAnnotation.R, vignettes/GeneAnswers/inst/doc/geneAnswers.R, vignettes/GeneAnswers/inst/doc/geneFunctionSummarize.R Package: GeneExpressionSignature Version: 1.4.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 Title: Gene Expression Signature based Similarity Metric Description: This package gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest. biocViews: Bioinformatics, GeneExpression Author: Yang Cao Maintainer: Yang Cao , Fei Li ,Lu Han MD5sum: 319d8966b4f6c28aebdbfa4f0b8c2d51 source.ver: src/contrib/GeneExpressionSignature_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneExpressionSignature_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneExpressionSignature_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneExpressionSignature_1.4.0.tgz vignettes: vignettes/GeneExpressionSignature/inst/doc/GeneExpressionSignature.pdf vignetteTitles: GeneExpressionSignature hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: genefilter Version: 1.40.0 Imports: AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10), graphics, methods, stats, survival Suggests: Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets, ALL, ROC License: Artistic-2.0 Archs: i386, x64 Title: genefilter: methods for filtering genes from microarray experiments Description: Some basic functions for filtering genes biocViews: Bioinformatics, Microarray Author: R. Gentleman, V. Carey, W. Huber, F. Hahne Maintainer: Bioconductor Package Maintainer MD5sum: 3bbb52c4acf1d83d58d45aa4b04397eb source.ver: src/contrib/genefilter_1.40.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genefilter_1.40.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genefilter_1.40.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genefilter_1.40.0.tgz vignettes: vignettes/genefilter/inst/doc/howtogenefilter.pdf, vignettes/genefilter/inst/doc/howtogenefinder.pdf, vignettes/genefilter/inst/doc/independent_filtering_plots.pdf vignetteTitles: Using the genefilter function to filter genes from a microarray dataset, How to find genes whose expression profile is similar to that of specified genes, Diagnostic plots for independent filtering hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genefilter/inst/doc/howtogenefilter.R, vignettes/genefilter/inst/doc/howtogenefinder.R, vignettes/genefilter/inst/doc/independent_filtering_plots.R dependsOnMe: a4Base, Agi4x44PreProcess, cellHTS, cellHTS2, charm, CNTools, eisa, GeneMeta, MLInterfaces, simpleaffy importsMe: affycoretools, affyQCReport, annmap, arrayQualityMetrics, Category, crlmm, DESeq, gCMAP, GGBase, GSRI, methyAnalysis, methylumi, phenoTest, Ringo, simpleaffy, tilingArray, XDE suggestsMe: AffyExpress, annotate, ArrayTools, BiocCaseStudies, BioNet, Category, categoryCompare, clusterStab, codelink, factDesign, ffpe, GOstats, GSEAlm, GSVA, logicFS, lumi, MCRestimate, oligo, oneChannelGUI, phyloseq, pvac, qpgraph, rtracklayer, siggenes, topGO, VanillaICE, XDE Package: genefu Version: 1.8.0 Depends: R (>= 2.10), survcomp, mclust, biomaRt Imports: amap Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable License: Artistic-2.0 Title: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer. Description: Description: This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, survival analysis, ... biocViews: DifferentialExpression, GeneExpression, Visualization, Clustering, Classification Author: Benjamin Haibe-Kains, Markus Schroeder, Gianluca Bontempi, Christos Sotiriou, John Quackenbush Maintainer: Benjamin Haibe-Kains , Markus Schroeder URL: http://compbio.dfci.harvard.edu MD5sum: d835843e4bce94d514911a91e2b82a57 source.ver: src/contrib/genefu_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genefu_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genefu_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genefu_1.8.0.tgz vignettes: vignettes/genefu/inst/doc/genefu.pdf vignetteTitles: genefu An Introduction (HowTo) hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genefu/inst/doc/genefu.R Package: GeneGA Version: 1.8.0 Depends: seqinr, hash, methods License: GPL version 2 Title: Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm Description: R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly. biocViews: GeneExpression Author: Zhenpeng Li, Fei Li, Xiaochen Bo and Shengqi Wang Maintainer: Zhenpeng Li URL: http://www.tbi.univie.ac.at/~ivo/RNA/ MD5sum: 9ebfbb148f3a5b04cc5f23a206223eba source.ver: src/contrib/GeneGA_1.8.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneGA_1.8.0.tgz vignettes: vignettes/GeneGA/inst/doc/GeneGA.pdf vignetteTitles: GeneGA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneGA/inst/doc/GeneGA.R Package: GeneGroupAnalysis Version: 1.4.0 Depends: R (>= 2.10), MCMCpack, GO.db, breastCancerVDX, rheumaticConditionWOLLBOLD, hgu133a.db, hgu133plus2.db Imports: AnnotationDbi, annotate, tcltk License: Artistic-2.0 Archs: i386, x64 Title: Gene Functional Class Analysis Description: R package providing functions to peform gene-set significance analysis over simple cross-sectional or time series data designs. biocViews: GeneExpression, DifferentialExpression, MultipleComparisons, CrossSectional, TimeCourse Author: Alejandro Quiroz-Zarate and John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ MD5sum: 378b3867ab1a93451ae09be732fb9049 source.ver: src/contrib/GeneGroupAnalysis_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneGroupAnalysis_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneGroupAnalysis_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneGroupAnalysis_1.4.0.tgz vignettes: vignettes/GeneGroupAnalysis/inst/doc/GeneGroupAnalysis.pdf vignetteTitles: GeneGroupAnalysis: a package for performance assessment and comparison for survival analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneGroupAnalysis/inst/doc/GeneGroupAnalysis.R Package: GeneMeta Version: 1.30.1 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 Title: MetaAnalysis for High Throughput Experiments Description: A collection of meta-analysis tools for analysing high throughput experimental data biocViews: Bioinformatics Author: Lara Lusa , R. Gentleman, M. Ruschhaupt Maintainer: Bioconductor Package Maintainer MD5sum: 6c44d7454be47eea7e6d117f7aab0bb0 source.ver: src/contrib/GeneMeta_1.30.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneMeta_1.30.1.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneMeta_1.30.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneMeta_1.30.1.tgz vignettes: vignettes/GeneMeta/inst/doc/GeneMeta.pdf vignetteTitles: GeneMeta Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneMeta/inst/doc/GeneMeta.R suggestsMe: genefu, XDE Package: GeneNetworkBuilder Version: 1.0.1 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13), graph Imports: plyr, graph LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, Rgraphviz, XML, RCytoscape License: GPL (>= 2) Archs: i386, x64 Title: Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data Description: Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF. biocViews: HighThroughputSequencing, Microarray, GraphsAndNetworks Author: Jianhong Ou and Lihua Julie Zhu Maintainer: Jianhong Ou MD5sum: e18243980ec2d371bcfd5470e6a85d60 source.ver: src/contrib/GeneNetworkBuilder_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneNetworkBuilder_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneNetworkBuilder_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneNetworkBuilder_1.0.1.tgz vignettes: vignettes/GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.pdf vignetteTitles: GeneNetworkBuilder Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.R Package: geneplotter Version: 1.36.0 Depends: R (>= 2.10),Biobase (>= 2.5.5), annotate, lattice Imports: annotate, AnnotationDbi, Biobase (>= 2.5.5), graphics, grDevices, grid, methods, RColorBrewer, stats, utils Suggests: Biobase (>= 2.5.5), Rgraphviz, annotate, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 Title: Graphics related functions for Bioconductor Description: Some basic functions for plotting genetic data biocViews: Visualization Author: R. Gentleman, Biocore Maintainer: Bioconductor Package Maintainer MD5sum: 94a3a993dcbc8facf2a77fb6e9753f50 source.ver: src/contrib/geneplotter_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/geneplotter_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/geneplotter_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/geneplotter_1.36.0.tgz vignettes: vignettes/geneplotter/inst/doc/byChroms.pdf, vignettes/geneplotter/inst/doc/visualize.pdf vignetteTitles: How to assemble a chromLocation object, Visualization of Microarray Data hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/geneplotter/inst/doc/byChroms.R, vignettes/geneplotter/inst/doc/visualize.R dependsOnMe: HMMcopy importsMe: biocGraph, DESeq, flowQ, IsoGeneGUI, RNAinteract, RNAither suggestsMe: BiocCaseStudies, biocGraph, Category, GOstats, maDB Package: geneRecommender Version: 1.30.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) Title: A gene recommender algorithm to identify genes coexpressed with a query set of genes Description: This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. biocViews: Microarray, Clustering Author: Gregory J. Hather , with contributions from Art B. Owen and Terence P. Speed Maintainer: Greg Hather MD5sum: a2d6d4b6166251bc05bb110749d9e65b source.ver: src/contrib/geneRecommender_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/geneRecommender_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/geneRecommender_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/geneRecommender_1.30.0.tgz vignettes: vignettes/geneRecommender/inst/doc/geneRecommender.pdf vignetteTitles: Using the geneRecommender Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/geneRecommender/inst/doc/geneRecommender.R Package: GeneRegionScan Version: 1.14.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) Title: GeneRegionScan Description: A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data. biocViews: Microarray, DataImport, SNP, OneChannel, Visualization Author: Lasse Folkersen, Diego Diez Maintainer: Lasse Folkersen MD5sum: 4136888cd305c99919d039a085622e99 source.ver: src/contrib/GeneRegionScan_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneRegionScan_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneRegionScan_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneRegionScan_1.14.0.tgz vignettes: vignettes/GeneRegionScan/inst/doc/GeneRegionScan.pdf vignetteTitles: GeneRegionScan hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneRegionScan/inst/doc/GeneRegionScan.R Package: GeneSelectMMD Version: 2.2.0 Depends: R (>= 2.13.2), Biobase Imports: Biobase, MASS, graphics, stats, survival, limma Suggests: ALL License: GPL (>= 2) Archs: i386, x64 Title: Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions Description: Gene selection based on a mixture of marginal distributions biocViews: Bioinformatics, DifferentialExpression Author: Jarrett Morrow , Weiliang Qiu , Wenqing He , Xiaogang Wang , Ross Lazarus . Maintainer: Weiliang Qiu MD5sum: a7df98bba98fa4379f0c4dd798b2fdc8 source.ver: src/contrib/GeneSelectMMD_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneSelectMMD_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneSelectMMD_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneSelectMMD_2.2.0.tgz vignettes: vignettes/GeneSelectMMD/inst/doc/GS207runTimesSim1k.pdf, vignettes/GeneSelectMMD/inst/doc/gsMMD.pdf vignetteTitles: GS207runTimesSim1k.pdf, Gene Selection based on a mixture of marginal distributions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneSelectMMD/inst/doc/gsMMD.R Package: GeneSelector Version: 2.8.0 Depends: R (>= 2.5.1), methods, stats, Biobase Imports: multtest, siggenes, samr, limma Suggests: multtest, siggenes, samr, limma License: GPL (>= 2) Archs: i386, x64 Title: Stability and Aggregation of ranked gene lists Description: The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis. biocViews: Statistics, DifferentialExpression Author: Martin Slawski , Anne-Laure Boulesteix . Maintainer: Martin Slawski MD5sum: d67f9c2d3c3149e1eae260942957782e source.ver: src/contrib/GeneSelector_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneSelector_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneSelector_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneSelector_2.8.0.tgz vignettes: vignettes/GeneSelector/inst/doc/GeneSelector.pdf vignetteTitles: GeneSelector.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneSelector/inst/doc/GeneSelector.R Package: GeneticsDesign Version: 1.26.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 Title: Functions for designing genetics studies Description: This package contains functions useful for designing genetics studies, including power and sample-size calculations. biocViews: Genetics Author: Gregory Warnes David Duffy , Michael Man Weiliang Qiu Ross Lazarus Maintainer: The R Genetics Project MD5sum: d2f7eb2ad56fe30a9e725d50c6e417f8 source.ver: src/contrib/GeneticsDesign_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneticsDesign_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneticsDesign_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneticsDesign_1.26.0.tgz vignettes: vignettes/GeneticsDesign/inst/doc/GPC.pdf vignetteTitles: Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeneticsDesign/inst/doc/GPC.R Package: GeneticsPed Version: 1.20.0 Depends: R (>= 2.4.0), gdata (>= 2.3.0), genetics (>= 1.3.0), MASS Suggests: RUnit, gtools License: LGPL (>= 2.1) Archs: i386, x64 Title: Pedigree and genetic relationship functions Description: Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care! biocViews: Genetics Author: Gregor Gorjanc and David A. Henderson , with code contributions by Brian Kinghorn and Andrew Percy (see file COPYING) Maintainer: David Henderson URL: http://rgenetics.org MD5sum: 836c6a7a1763853aa6642ab6899fc63e source.ver: src/contrib/GeneticsPed_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneticsPed_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneticsPed_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneticsPed_1.20.0.tgz vignettes: vignettes/GeneticsPed/inst/doc/geneticRelatedness.pdf, vignettes/GeneticsPed/inst/doc/pedigreeHandling.pdf, vignettes/GeneticsPed/inst/doc/quanGenAnimalModel.pdf vignetteTitles: Calculation of genetic relatedness/relationship between individuals in the pedigree, Pedigree handling, Quantitative genetic (animal) model example in R hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GeneticsPed/inst/doc/geneticRelatedness.R, vignettes/GeneticsPed/inst/doc/pedigreeHandling.R, vignettes/GeneticsPed/inst/doc/quanGenAnimalModel.R Package: genoCN Version: 1.10.0 Imports: graphics, stats, utils License: GPL (>=2) Archs: i386, x64 Title: genotyping and copy number study tools Description: Simultaneous identification of copy number states and genotype calls for regions of either copy number variations or copy number aberrations biocViews: Microarray, Genetics Author: Wei Sun and ZhengZheng Tang Maintainer: Wei Sun MD5sum: 2a930ff589391326923dc9a56dcd42ae source.ver: src/contrib/genoCN_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genoCN_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genoCN_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genoCN_1.10.0.tgz vignettes: vignettes/genoCN/inst/doc/genoCN.pdf vignetteTitles: add stuff hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genoCN/inst/doc/genoCN.R Package: GenomeGraphs Version: 1.18.0 Depends: R (>= 2.10), methods, biomaRt, grid License: Artistic-2.0 Title: Plotting genomic information from Ensembl Description: Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system. biocViews: Visualization, Microarray Author: Steffen Durinck , James Bullard Maintainer: Steffen Durinck MD5sum: 1e5eb419fb1d1c3251524f648ae44f7f source.ver: src/contrib/GenomeGraphs_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GenomeGraphs_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GenomeGraphs_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GenomeGraphs_1.18.0.tgz vignettes: vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf vignetteTitles: The GenomeGraphs users guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GenomeGraphs/inst/doc/GenomeGraphs.R dependsOnMe: Genominator, waveTiling suggestsMe: rMAT Package: genomeIntervals Version: 1.14.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.13.3), BiocGenerics (>= 0.3.2) Imports: methods, Biobase License: Artistic-2.0 Title: Operations on genomic intervals Description: This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'. biocViews: DataImport, Infrastructure, Genetics Author: Julien Gagneur , Joern Toedling, Richard Bourgon, Nicolas Delhomme Maintainer: Julien Gagneur MD5sum: 6c8e7ac7a71cc785e5c225647b343f44 source.ver: src/contrib/genomeIntervals_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genomeIntervals_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genomeIntervals_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genomeIntervals_1.14.0.tgz vignettes: vignettes/genomeIntervals/inst/doc/genomeIntervals.pdf vignetteTitles: Overview of the genomeIntervals package. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genomeIntervals/inst/doc/genomeIntervals.R dependsOnMe: easyRNASeq, girafe, HiTC Package: genomes Version: 2.4.0 Depends: R (>= 2.10), XML, RCurl, GenomicRanges, IRanges, Biostrings License: Artistic-2.0 Title: Genome sequencing project metadata Description: Collects genome sequencing project data from NCBI and the ENA. biocViews: Annotation, Genetics Author: Chris Stubben Maintainer: Chris Stubben MD5sum: f3d65fb7d2ce23674b1be04acba9d921 source.ver: src/contrib/genomes_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genomes_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genomes_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genomes_2.4.0.tgz vignettes: vignettes/genomes/inst/doc/genome-tables.pdf vignetteTitles: Introduction to genome projects hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genomes/inst/doc/genome-tables.R Package: GenomicFeatures Version: 1.10.2 Depends: BiocGenerics (>= 0.1.0), IRanges (>= 1.15.35), GenomicRanges (>= 1.9.66), AnnotationDbi (>= 1.19.36) Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics, IRanges, GenomicRanges, Biostrings (>= 2.23.2), rtracklayer (>= 1.15.1), biomaRt, RCurl, utils, Biobase (>= 2.15.1) Suggests: rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14), BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), Rsamtools, pasillaBamSubset (>= 0.0.5), RUnit License: Artistic-2.0 Title: Tools for making and manipulating transcript centric annotations Description: A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format. biocViews: Genetics, Infrastructure, Annotation, HighThroughputSequencing Author: M. Carlson, H. Pages, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence Maintainer: Bioconductor Package Maintainer MD5sum: 725df17052211788f6c5e6752676b412 source.ver: src/contrib/GenomicFeatures_1.10.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/GenomicFeatures_1.10.2.zip win64.binary.ver: bin/windows64/contrib/2.15/GenomicFeatures_1.10.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GenomicFeatures_1.10.2.tgz vignettes: vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf vignetteTitles: Making and Utilizing TranscriptDb Objects hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GenomicFeatures/inst/doc/GenomicFeatures.R, vignettes/GenomicFeatures/inst/doc/spliceGraph.R dependsOnMe: OrganismDbi importsMe: biovizBase, ggbio, gmapR, Gviz, HTSeqGenie, methyAnalysis, VariantAnnotation, VariantTools suggestsMe: Biostrings, chipseq, easyRNASeq, GenomicRanges, Gviz, HTSeqGenie, MiRaGE, Rsamtools, ShortRead Package: GenomicRanges Version: 1.10.7 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.12), IRanges (>= 1.15.42) Imports: methods, utils, BiocGenerics, IRanges LinkingTo: IRanges Suggests: Biostrings (>= 2.25.3), Rsamtools (>= 1.9.21), BSgenome, rtracklayer, GenomicFeatures, VariantAnnotation, edgeR, DESeq, DEXSeq, EatonEtAlChIPseq (>= 0.0.3), leeBamViews, pasilla, pasillaBamSubset, org.Sc.sgd.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Dmelanogaster.UCSC.dm3, RUnit, digest License: Artistic-2.0 Archs: i386, x64 Title: Representation and manipulation of genomic intervals Description: The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. biocViews: Genetics, Sequencing, HighThroughputSequencing, Annotation Author: P. Aboyoun, H. Pages and M. Lawrence Maintainer: Bioconductor Package Maintainer MD5sum: c0cea669b165acc0e6498e0345e916c4 source.ver: src/contrib/GenomicRanges_1.10.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/GenomicRanges_1.10.7.zip win64.binary.ver: bin/windows64/contrib/2.15/GenomicRanges_1.10.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GenomicRanges_1.10.7.tgz vignettes: vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf, vignettes/GenomicRanges/inst/doc/GenomicRangesUseCases.pdf, vignettes/GenomicRanges/inst/doc/OverlapEncodings.pdf, vignettes/GenomicRanges/inst/doc/summarizeOverlaps-modes.pdf, vignettes/GenomicRanges/inst/doc/summarizeOverlaps.pdf vignetteTitles: An Introduction to GenomicRanges, GenomicRanges Use Cases, Overlap encodings, summarizeOverlaps-modes.pdf, Overview of summarizeOverlaps hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GenomicRanges/inst/doc/GenomicRangesUseCases.R, vignettes/GenomicRanges/inst/doc/OverlapEncodings.R, vignettes/GenomicRanges/inst/doc/summarizeOverlaps.R dependsOnMe: annmap, BSgenome, bsseq, chipseq, cn.mops, CSAR, deepSNV, DiffBind, easyRNASeq, exomeCopy, fastseg, genomes, GenomicFeatures, genoset, GGtools, gmapR, gwascat, htSeqTools, minfi, PING, Rcade, Repitools, Rsamtools, rSFFreader, rtracklayer, segmentSeq, seqbias, ShortRead, VariantAnnotation, VariantTools importsMe: ArrayExpressHTS, biovizBase, chipseq, ChIPseqR, FunciSNP, GenomicFeatures, genoset, ggbio, gmapR, Gviz, HTSeqGenie, methyAnalysis, MinimumDistance, NarrowPeaks, nucleR, oligoClasses, PICS, Repitools, rnaSeqMap, Rsamtools, rSFFreader, rtracklayer, segmentSeq, ShortRead, SNPchip, VanillaICE, VariantTools, waveTiling suggestsMe: BiocGenerics, IRanges, MiRaGE, NarrowPeaks, Repitools Package: Genominator Version: 1.12.0 Depends: R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics (>= 0.1.0), IRanges, GenomeGraphs Imports: graphics, stats, utils Suggests: biomaRt, ShortRead, yeastRNASeq License: Artistic-2.0 Title: Analyze, manage and store genomic data Description: Tools for storing, accessing, analyzing and visualizing genomic data. biocViews: Infrastructure Author: James Bullard, Kasper Daniel Hansen Maintainer: James Bullard MD5sum: e53345554364e32d5cd8705b40485c8b source.ver: src/contrib/Genominator_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Genominator_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Genominator_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Genominator_1.12.0.tgz vignettes: vignettes/Genominator/inst/doc/Genominator.pdf, vignettes/Genominator/inst/doc/plotting.pdf, vignettes/Genominator/inst/doc/withShortRead.pdf vignetteTitles: The Genominator User Guide, Plotting with Genominator, Working with the ShortRead Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Genominator/inst/doc/Genominator.R, vignettes/Genominator/inst/doc/plotting.R, vignettes/Genominator/inst/doc/withShortRead.R suggestsMe: oneChannelGUI Package: genoset Version: 1.10.1 Depends: R (>= 2.10), BiocGenerics (>= 0.1.6), Biobase (>= 2.15.1), IRanges (>= 1.13.5), GenomicRanges Imports: methods, graphics, GenomicRanges Suggests: RUnit, DNAcopy, stats Enhances: parallel License: Artistic-2.0 Archs: i386, x64 Title: Provides classes similar to ExpressionSet for copy number analysis Description: Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a "locData" slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. biocViews: Infrastructure, DataRepresentation, Microarray, SNP, CopyNumberVariants Author: Peter M. Haverty Maintainer: Peter M. Haverty MD5sum: f5867ab1dc2e5b58d03ba64de4d1257e source.ver: src/contrib/genoset_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/genoset_1.10.1.zip win64.binary.ver: bin/windows64/contrib/2.15/genoset_1.10.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genoset_1.10.1.tgz vignettes: vignettes/genoset/inst/doc/genoset.pdf vignetteTitles: genoset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genoset/inst/doc/genoset.R dependsOnMe: VegaMC importsMe: methyAnalysis Package: GEOmetadb Version: 1.18.0 Depends: GEOquery,RSQLite License: Artistic-2.0 Title: A compilation of metadata from NCBI GEO Description: The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 . biocViews: Infrastructure Author: Jack Zhu and Sean Davis Maintainer: Jack Zhu URL: http://gbnci.abcc.ncifcrf.gov/geo/ MD5sum: 0db43d7953d44a75b352241b6ad20c8b source.ver: src/contrib/GEOmetadb_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GEOmetadb_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GEOmetadb_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GEOmetadb_1.18.0.tgz vignettes: vignettes/GEOmetadb/inst/doc/GEOmetadb_diagram.pdf, vignettes/GEOmetadb/inst/doc/GEOmetadb.pdf vignetteTitles: GEOmetadb_diagram.pdf, GEOmetadb hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GEOmetadb/inst/doc/GEOmetadb.R Package: GEOquery Version: 2.24.1 Depends: methods, Biobase Imports: XML, RCurl Suggests: limma, RUnit License: GPL-2 Title: Get data from NCBI Gene Expression Omnibus (GEO) Description: The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor. biocViews: Microarray, DataImport, OneChannel, TwoChannel, SAGE Author: Sean Davis Maintainer: Sean Davis URL: http://watson.nci.nih.gov/~sdavis MD5sum: 8deff757b1a4c675effab8917188c10d source.ver: src/contrib/GEOquery_2.24.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/GEOquery_2.24.1.zip win64.binary.ver: bin/windows64/contrib/2.15/GEOquery_2.24.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GEOquery_2.24.1.tgz vignettes: vignettes/GEOquery/inst/doc/GEOquery.pdf vignetteTitles: GEOquery hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GEOquery/inst/doc/GEOquery.R importsMe: ChIPXpress, SRAdb, virtualArray suggestsMe: dyebias, PGSEA Package: GEOsubmission Version: 1.10.0 Imports: affy, Biobase, utils License: GPL (>= 2) Title: Prepares microarray data for submission to GEO Description: Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit). biocViews: Microarray Author: Alexandre Kuhn Maintainer: Alexandre Kuhn MD5sum: cd66fee62236043fe89d34589a480628 source.ver: src/contrib/GEOsubmission_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GEOsubmission_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GEOsubmission_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GEOsubmission_1.10.0.tgz vignettes: vignettes/GEOsubmission/inst/doc/GEOsubmission.pdf vignetteTitles: GEOsubmission Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GEOsubmission/inst/doc/GEOsubmission.R Package: GEWIST Version: 1.2.0 Depends: R (>= 2.10), car License: GPL-2 Title: Gene Environment Wide Interaction Search Threshold Description: This 'GEWIST' package provides statistical tools to efficiently optimize SNP prioritization for gene-gene and gene-environment interactions. biocViews: Bioinformatics, MultipleComparisons, BiologicalDomains, Genetics Author: Wei Q. Deng, Guillaume Pare Maintainer: Wei Q. Deng MD5sum: 5af819424b4fefb8adc08ba1ef1a3e0b source.ver: src/contrib/GEWIST_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GEWIST_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GEWIST_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GEWIST_1.2.0.tgz vignettes: vignettes/GEWIST/inst/doc/GEWIST.pdf vignetteTitles: GEWIST.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GEWIST/inst/doc/GEWIST.R Package: GGBase Version: 3.20.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, Matrix, AnnotationDbi License: Artistic-2.0 Title: GGBase infrastructure for genetics of gene expression package GGtools Description: infrastructure Author: VJ Carey Maintainer: VJ Carey MD5sum: 655d313e34843e6532d34e9f7c5c8f4a source.ver: src/contrib/GGBase_3.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GGBase_3.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GGBase_3.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GGBase_3.20.0.tgz vignettes: vignettes/GGBase/inst/doc/ggbase.pdf vignetteTitles: GGBase -- infrastructure for GGtools,, genetics of gene expression hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GGBase/inst/doc/ggbase.R dependsOnMe: GGtools importsMe: qpgraph Package: ggbio Version: 1.6.6 Depends: methods, ggplot2 (>= 0.9.2) Imports: methods, biovizBase(>= 1.5.9), reshape2, gtable, ggplot2(>= 0.9.2), BiocGenerics, Biobase, IRanges, GenomicRanges, GenomicFeatures, Rsamtools, BSgenome, gridExtra, scales, plyr, VariantAnnotation, Hmisc, rtracklayer Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, affyPLM, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr License: Artistic-2.0 Title: Static visualization for genomic data. Description: The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. biocViews: Infrastructure, Visualization, Bioinformatics Author: Tengfei Yin, Dianne Cook, Michael Lawrence Maintainer: Tengfei Yin URL: http://tengfei.github.com/ggbio/ MD5sum: 89b73a756bf8379858aa7d14ef9bb02a source.ver: src/contrib/ggbio_1.6.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/ggbio_1.6.6.zip win64.binary.ver: bin/windows64/contrib/2.15/ggbio_1.6.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ggbio_1.6.6.tgz vignettes: vignettes/ggbio/inst/doc/ggbio.pdf vignetteTitles: ggbio hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ggbio/inst/doc/autoplot.R, vignettes/ggbio/inst/doc/chip-seq.R, vignettes/ggbio/inst/doc/circular.R, vignettes/ggbio/inst/doc/fake.R, vignettes/ggbio/inst/doc/ggbio.R, vignettes/ggbio/inst/doc/ideogram.R, vignettes/ggbio/inst/doc/intro.R, vignettes/ggbio/inst/doc/karyogram.R, vignettes/ggbio/inst/doc/Manhattan.R, vignettes/ggbio/inst/doc/mismatch.R, vignettes/ggbio/inst/doc/rangeslinkedtodata.R, vignettes/ggbio/inst/doc/tracks.R, vignettes/ggbio/inst/doc/txdb.R suggestsMe: gwascat Package: GGtools Version: 4.6.2 Depends: R (>= 2.14), stats4, GGBase (>= 3.19.7), IRanges, GenomicRanges, Rsamtools Imports: methods, utils, stats, BiocGenerics, snpStats, ff, AnnotationDbi, Biobase, bit, VariantAnnotation Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP.20111119 Enhances: MatrixEQTL License: Artistic-2.0 Title: software and data for analyses in genetics of gene expression Description: software and data for analyses in genetics of gene expression biocViews: Genetics, GeneExpression, GeneticVariability, SNP Author: VJ Carey Maintainer: VJ Carey MD5sum: bc707b416bad4184abdbfd7082cfaf10 source.ver: src/contrib/GGtools_4.6.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/GGtools_4.6.2.zip win64.binary.ver: bin/windows64/contrib/2.15/GGtools_4.6.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GGtools_4.6.2.tgz vignettes: vignettes/GGtools/inst/doc/GGtools_2012.pdf vignetteTitles: GGtools 2012: efficient tools for eQTL discovery hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GGtools/inst/doc/GGtools_2012.R Package: girafe Version: 1.10.1 Depends: R (>= 2.10.0), methods, IRanges (>= 1.3.53), Rsamtools, ShortRead (>= 1.3.21), intervals (>= 0.13.1), genomeIntervals (>= 1.7.3), grid Imports: methods, Biobase, Biostrings, BSgenome, graphics, grDevices, stats, utils, IRanges Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 Archs: i386, x64 Title: Genome Intervals and Read Alignments for Functional Exploration Description: The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals. biocViews: Sequencing, HighThroughputSequencing Author: Joern Toedling, with contributions from Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang Huber Maintainer: J. Toedling MD5sum: c01b324a16c996fbfe68b2787508f619 source.ver: src/contrib/girafe_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/girafe_1.10.1.zip win64.binary.ver: bin/windows64/contrib/2.15/girafe_1.10.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/girafe_1.10.1.tgz vignettes: vignettes/girafe/inst/doc/girafe.pdf vignetteTitles: Genome intervals and read alignments for functional exploration hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/girafe/inst/doc/girafe.R dependsOnMe: HiTC Package: GLAD Version: 2.20.0 Depends: R (>= 2.10) Suggests: aws, tcltk License: GPL-2 Archs: i386, x64 Title: Gain and Loss Analysis of DNA Description: Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified. biocViews: Microarray, CopyNumberVariants Author: Philippe Hupe Maintainer: Philippe Hupe URL: http://bioinfo.curie.fr SystemRequirements: gsl. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. MD5sum: 2f4891c5cfd0600138ff1b022aba52df source.ver: src/contrib/GLAD_2.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GLAD_2.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GLAD_2.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GLAD_2.20.0.tgz vignettes: vignettes/GLAD/inst/doc/GLAD.pdf vignetteTitles: GLAD hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GLAD/inst/doc/GLAD.R dependsOnMe: ITALICS, MANOR importsMe: ITALICS, MANOR, snapCGH suggestsMe: ADaCGH2 Package: GlobalAncova Version: 3.26.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi Suggests: Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db, vsn, GSEABase, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Title: Calculates a global test for differential gene expression between groups Description: We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany. biocViews: Microarray, OneChannel, Bioinformatics, DifferentialExpression, Pathways Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with contributions from S. Knueppel Maintainer: Manuela Hummel MD5sum: 7b135f31e21927e49107920287fddbf5 source.ver: src/contrib/GlobalAncova_3.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GlobalAncova_3.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GlobalAncova_3.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GlobalAncova_3.26.0.tgz vignettes: vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.pdf, vignettes/GlobalAncova/inst/doc/GlobalAncova.pdf vignetteTitles: GlobalAncovaDecomp.pdf, GlobalAncova.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.R, vignettes/GlobalAncova/inst/doc/GlobalAncova.R Package: globaltest Version: 5.12.0 Depends: methods Imports: Biobase (>= 2.5.5), survival, AnnotationDbi, annotate, multtest, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, annotate, Biobase (>= 2.5.5), survival, GSEABase, penalized, gss, MASS, boot, rpart License: GPL (>= 2) Title: Testing groups of covariates/features for association with a response variable, with applications to gene set testing Description: The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. biocViews: Microarray, OneChannel, Bioinformatics, DifferentialExpression, GO, Pathways Author: Jelle Goeman and Jan Oosting, with contributions by Livio Finos and Aldo Solari Maintainer: Jelle Goeman URL: http://www.msbi.nl/goeman MD5sum: 36957526c7ef9ca69931596b22f00a96 source.ver: src/contrib/globaltest_5.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/globaltest_5.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/globaltest_5.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/globaltest_5.12.0.tgz vignettes: vignettes/globaltest/inst/doc/GlobalTest.pdf vignetteTitles: Global Test hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/globaltest/inst/doc/GlobalTest_deprecated.R, vignettes/globaltest/inst/doc/GlobalTest.R dependsOnMe: GlobalAncova importsMe: SIM suggestsMe: topGO Package: gmapR Version: 1.0.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges, GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 Title: Provides convenience methods to work with GMAP and GSNAP from within R Description: GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool. Author: Cory Barr, Thomas Wu, Michael Lawrence Maintainer: Cory Barr MD5sum: 0a8cd0a1ff17ec52c5665ceae6228a90 source.ver: src/contrib/gmapR_1.0.0.tar.gz vignettes: vignettes/gmapR/inst/doc/gmapR.pdf vignetteTitles: gmapR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gmapR/inst/doc/gmapR.R dependsOnMe: HTSeqGenie importsMe: VariantTools Package: GOFunction Version: 1.4.0 Depends: R (>= 2.11.0), methods, Biobase (>= 2.8.0), graph (>= 1.26.0), Rgraphviz (>= 1.26.0), GO.db (>= 2.4.1), AnnotationDbi (>= 1.10.2), SparseM (>= 0.85) Imports: methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, SparseM License: GPL (>= 2) Title: GO-function: deriving biologcially relevant functions from statistically significant functions Description: The GO-function package provides a tool to address the redundancy that result from the GO structure or multiple annotation genes and derive biologically relevant functions from the statistically significant functions based on some intuitive assumption and statistical testing. biocViews: GO, Pathways, Microarray, GeneSetEnrichment Author: Jing Wang Maintainer: Zheng Guo MD5sum: 312ae67efb12ffe8b727f53478b44273 source.ver: src/contrib/GOFunction_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GOFunction_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GOFunction_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GOFunction_1.4.0.tgz vignettes: vignettes/GOFunction/inst/doc/GOFunction.pdf vignetteTitles: GO-function hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GOFunction/inst/doc/GOFunction.R Package: goProfiles Version: 1.20.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db License: GPL-2 Title: goProfiles: an R package for the statistical analysis of functional profiles Description: The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'. biocViews: Microarray, GO Author: Alex Sanchez, Jordi Ocana and Miquel Salicru Maintainer: Alex Sanchez MD5sum: 6b04464d9c10553a880adce884ca7e32 source.ver: src/contrib/goProfiles_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/goProfiles_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/goProfiles_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/goProfiles_1.20.0.tgz vignettes: vignettes/goProfiles/inst/doc/goProfiles.pdf vignetteTitles: goProfiles Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/goProfiles/inst/doc/goProfiles.R Package: GOSemSim Version: 1.16.1 Depends: R (>= 2.10), Rcpp Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db LinkingTo: Rcpp Suggests: DOSE, clusterProfiler License: GPL-2 Archs: i386, x64 Title: GO-terms Semantic Similarity Measures Description: Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for estimating GO semantic similarities. Support many species, including Anopheles, Arabidopsis, Bovine, Canine, Chicken, Chimp, Coelicolor, E coli strain K12 and Sakai, Fly, Human, Malaria, Mouse, Pig, Rhesus, Rat, Worm, Xenopus, Yeast, and Zebrafish. biocViews: GO, Clustering, Pathways, NetworkAnalysis Author: Guangchuang Yu Maintainer: Guangchuang Yu URL: http://bioinformatics.oxfordjournals.org/content/26/7/976.full MD5sum: bf4823b5f8d58a24aaf2d4f62e995edb source.ver: src/contrib/GOSemSim_1.16.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/GOSemSim_1.16.1.zip win64.binary.ver: bin/windows64/contrib/2.15/GOSemSim_1.16.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GOSemSim_1.16.1.tgz vignettes: vignettes/GOSemSim/inst/doc/GOSemSim.pdf vignetteTitles: An introduction to GOSemSim hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GOSemSim/inst/doc/GOSemSim.R importsMe: DOSE suggestsMe: clusterProfiler, ReactomePA Package: goseq Version: 1.10.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase Imports: mgcv, graphics, stats, utils, AnnotationDbi Suggests: GO.db, edgeR, org.Hs.eg.db License: LGPL (>= 2) Title: Gene Ontology analyser for RNA-seq and other length biased data Description: Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data biocViews: HighThroughputSequencingData, GO, GeneExpression, Transcription, RNAseq Author: Matthew Young Maintainer: Matthew Young , Nadia Davidson MD5sum: 4568343d70df2b15964fbc3316d7676b source.ver: src/contrib/goseq_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/goseq_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/goseq_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/goseq_1.10.0.tgz vignettes: vignettes/goseq/inst/doc/goseq.pdf vignetteTitles: goseq User's Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/goseq/inst/doc/goseq.R suggestsMe: oneChannelGUI Package: GOstats Version: 2.24.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.3.26), graph Imports: AnnotationDbi (>= 0.0.89), Biobase (>= 1.15.29), Category (>= 2.3.26), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), graph (>= 1.15.15), methods, stats , AnnotationForge Suggests: hgu95av2.db (>= 1.13.0), ALL, GO.db (>= 1.13.0), annotate, multtest, genefilter, RColorBrewer, Rgraphviz, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 Title: Tools for manipulating GO and microarrays. Description: A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations. biocViews: Bioinformatics, Annotation, GO, MultipleComparisons Author: R. Gentleman and S. Falcon Maintainer: Bioconductor Package Maintainer MD5sum: 7530e5a062aa69555de8aaa00ac200a5 source.ver: src/contrib/GOstats_2.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GOstats_2.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GOstats_2.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GOstats_2.24.0.tgz vignettes: vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf, vignettes/GOstats/inst/doc/GOstatsHyperG.pdf, vignettes/GOstats/inst/doc/GOvis.pdf vignetteTitles: Hypergeometric tests for less common model organisms, Hypergeometric Tests Using GOstats, Visualizing Data Using GOstats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GOstats/inst/doc/GOstatsHyperG.R, vignettes/GOstats/inst/doc/GOvis.R dependsOnMe: attract importsMe: affycoretools, attract, categoryCompare suggestsMe: BiocCaseStudies, Category, eisa, GSEAlm, HTSanalyzeR, MLP, MmPalateMiRNA, oneChannelGUI, phenoDist, qpgraph, safe Package: goTools Version: 1.32.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 Title: Functions for Gene Ontology database Description: Wraper functions for description/comparison of oligo ID list using Gene Ontology database biocViews: Microarray,GO,Visualization Author: Yee Hwa (Jean) Yang , Agnes Paquet Maintainer: Agnes Paquet MD5sum: bf402f36354117cee1b0cc136a8464d8 source.ver: src/contrib/goTools_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/goTools_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/goTools_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/goTools_1.32.0.tgz vignettes: vignettes/goTools/inst/doc/goTools.pdf vignetteTitles: goTools overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/goTools/inst/doc/goTools.R Package: gpls Version: 1.30.0 Imports: stats Suggests: MASS License: Artistic-2.0 Title: Classification using generalized partial least squares Description: Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification. biocViews: Bioinformatics, Classification, Microarray Author: Beiying Ding Maintainer: Bioconductor Package Maintainer MD5sum: 6749928553dfd26d6c2de3c1847717d9 source.ver: src/contrib/gpls_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gpls_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gpls_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gpls_1.30.0.tgz vignettes: vignettes/gpls/inst/doc/gpls.pdf vignetteTitles: gpls Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gpls/inst/doc/gpls.R suggestsMe: MCRestimate, MLInterfaces Package: gprege Version: 1.2.0 Depends: R (>= 2.8.0), gptk Suggests: spam License: AGPL-3 Title: Gaussian Process Ranking and Estimation of Gene Expression time-series Description: The gprege package implements the methodology described in Kalaitzis & Lawrence (2011) "A simple approach to ranking differentially expressed gene expression time-courses through Gaussian process regression". The software fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimised via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via ROC curves is performed against BATS (Angelini et.al, 2007). A detailed discussion of the ranking approach and dataset used can be found in the paper (http://www.biomedcentral.com/1471-2105/12/180). biocViews: Microarray, Preprocessing, Bioinformatics, DifferentialExpression, TimeCourse Author: Alfredo A. Kalaitzis Maintainer: Alfredo A. Kalaitzis URL: http://staffwww.dcs.shef.ac.uk/people/A.Kalaitzis/ MD5sum: 367a3ccd7ab91b35a690575d421045b3 source.ver: src/contrib/gprege_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gprege_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gprege_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gprege_1.2.0.tgz vignettes: vignettes/gprege/inst/doc/gprege_quick.pdf vignetteTitles: gprege Quick Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gprege/inst/doc/gprege_quick.R Package: graph Version: 1.36.2 Depends: R (>= 2.10), methods Imports: methods, stats, stats4, tools, utils, BiocGenerics (>= 0.1.11) Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster Enhances: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Title: graph: A package to handle graph data structures Description: A package that implements some simple graph handling capabilities. biocViews: GraphsAndNetworks Author: R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon Maintainer: Bioconductor Package Maintainer MD5sum: bf25376c51b9bb8fb67765c10bb6f765 source.ver: src/contrib/graph_1.36.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/graph_1.36.2.zip win64.binary.ver: bin/windows64/contrib/2.15/graph_1.36.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/graph_1.36.2.tgz vignettes: vignettes/graph/inst/doc/clusterGraph.pdf, vignettes/graph/inst/doc/graphAttributes.pdf, vignettes/graph/inst/doc/GraphClass.pdf, vignettes/graph/inst/doc/graph.pdf, vignettes/graph/inst/doc/MultiGraphClass.pdf vignetteTitles: clusterGraph and distGraph, Attributes for Graph Objects, Graph Design, Graph, graphBAM and MultiGraph classes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/graph/inst/doc/clusterGraph.R, vignettes/graph/inst/doc/graphAttributes.R, vignettes/graph/inst/doc/GraphClass.R, vignettes/graph/inst/doc/graph.R, vignettes/graph/inst/doc/MultiGraphClass.R dependsOnMe: apComplex, biocGraph, BioMVCClass, BioNet, CellNOptR, ddgraph, flowWorkspace, gage, gaggle, GeneNetworkBuilder, GOFunction, GOstats, GraphAT, graphite, GSEABase, gwascat, hyperdraw, hypergraph, KEGGgraph, maigesPack, NCIgraph, nem, netresponse, pathRender, pkgDepTools, RbcBook1, RBGL, RBioinf, RCytoscape, Rgraphviz, RpsiXML, Rtreemix, SRAdb, topGO importsMe: biocGraph, biocViews, CAMERA, Category, categoryCompare, DEGraph, flowCore, flowUtils, flowWorkspace, GeneAnswers, GeneNetworkBuilder, GOFunction, GOstats, GraphAT, graphite, GSEABase, HTSanalyzeR, KEGGgraph, keggorthology, NCIgraph, nem, OrganismDbi, PCpheno, pkgDepTools, ppiStats, qpgraph, RchyOptimyx, Rgraphviz, rsbml, Rtreemix, Streamer, topGO suggestsMe: BiocCaseStudies, Category, categoryCompare, DEGraph, EBcoexpress, ecolitk, MmPalateMiRNA, qpgraph, SPIA Package: GraphAlignment Version: 1.20.0 License: file LICENSE Archs: i386, x64 Title: GraphAlignment Description: Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006)) biocViews: GraphsAndNetworks, NetworkAnalysis Author: Joern P. Meier , Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg. Maintainer: Joern P. Meier URL: http://www.thp.uni-koeln.de/~berg/GraphAlignment/ MD5sum: 4c21615b1f2f837a88c275bbec81a390 source.ver: src/contrib/GraphAlignment_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GraphAlignment_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GraphAlignment_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GraphAlignment_1.20.0.tgz vignettes: vignettes/GraphAlignment/inst/doc/align_principle2b1.pdf, vignettes/GraphAlignment/inst/doc/align_principle2c1.pdf, vignettes/GraphAlignment/inst/doc/align_principle_short1.pdf, vignettes/GraphAlignment/inst/doc/a.pdf, vignettes/GraphAlignment/inst/doc/binning-01a.pdf, vignettes/GraphAlignment/inst/doc/GraphAlignment.pdf vignetteTitles: align_principle2b1.pdf, align_principle2c1.pdf, align_principle_short1.pdf, a.pdf, binning-01a.pdf, GraphAlignment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GraphAlignment/inst/doc/GraphAlignment.R Package: GraphAT Version: 1.30.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL Title: Graph Theoretic Association Tests Description: Functions and data used in Balasubramanian, et al. (2004) biocViews: NetworkAnalysis, GraphsAndNetworks Author: R. Balasubramanian, T. LaFramboise, D. Scholtens Maintainer: Thomas LaFramboise MD5sum: 0eea2a26fbe273097cb1d6a4612ae03f source.ver: src/contrib/GraphAT_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GraphAT_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GraphAT_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GraphAT_1.30.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: graphite Version: 1.4.0 Depends: R (>= 2.10), graph Imports: AnnotationDbi, graph, graphics, methods, org.Hs.eg.db, stats, utils Suggests: DEGraph (>= 1.4), hgu133plus2.db, RCytoscape (>= 1.6), SPIA (>= 2.2), topologyGSA (>= 1.0) License: AGPL-3 Title: GRAPH Interaction from pathway Topological Environment Description: Graph objects from pathway topology derived from NCI, KEGG, Biocarta and Reactome databases. biocViews: Pathways, ConnectTools, GraphsAndNetworks Author: Gabriele Sales , Enrica Calura , Chiara Romualdi Maintainer: Gabriele Sales MD5sum: b843bdd5db84a6a719336fd719bc3f0f source.ver: src/contrib/graphite_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/graphite_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/graphite_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/graphite_1.4.0.tgz vignettes: vignettes/graphite/inst/doc/graphite.pdf vignetteTitles: GRAPH Interaction from pathway Topological Environment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/graphite/inst/doc/graphite.R Package: GRENITS Version: 1.10.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) Archs: i386, x64 Title: Gene Regulatory Network Inference Using Time Series Description: The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model. biocViews: NetworkInference, GeneRegulation, TimeCourse, GraphsAndNetworks Author: Edward Morrissey Maintainer: Edward Morrissey MD5sum: f608423bca1f467bd1572422125fcab4 source.ver: src/contrib/GRENITS_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GRENITS_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GRENITS_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GRENITS_1.10.0.tgz vignettes: vignettes/GRENITS/inst/doc/GRENITS_package.pdf vignetteTitles: GRENITS hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GRENITS/inst/doc/GRENITS_package.R Package: GSEABase Version: 1.20.2 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), annotate, methods, graph Imports: BiocGenerics, annotate, AnnotationDbi, Biobase, graph, methods, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz License: Artistic-2.0 Title: Gene set enrichment data structures and methods Description: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). biocViews: Infrastructure, Bioinformatics Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer: Bioconductor Package Maintainer MD5sum: 6eb22d9195f1d742afd9cb087031d179 source.ver: src/contrib/GSEABase_1.20.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSEABase_1.20.2.zip win64.binary.ver: bin/windows64/contrib/2.15/GSEABase_1.20.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSEABase_1.20.2.tgz vignettes: vignettes/GSEABase/inst/doc/GSEABase.pdf vignetteTitles: An introduction to GSEABase hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSEABase/inst/doc/GSEABase.R dependsOnMe: AGDEX, BicARE, gCMAP, GSVA, PROMISE importsMe: Category, categoryCompare, cellHTS2, GSRI, GSVA, HTSanalyzeR, PCpheno, phenoTest, PROMISE, ReportingTools suggestsMe: BiocCaseStudies, categoryCompare, gage, GlobalAncova, globaltest, GOstats, PGSEA, phenoTest Package: GSEAlm Version: 1.18.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 Title: Linear Model Toolset for Gene Set Enrichment Analysis Description: Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics. biocViews: Microarray, Bioinformatics Author: Assaf Oron, Robert Gentleman (with contributions from S. Falcon and Z. Jiang) Maintainer: Assaf Oron MD5sum: 5918af9b11bc6ad26c64398bd760a746 source.ver: src/contrib/GSEAlm_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSEAlm_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GSEAlm_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSEAlm_1.18.0.tgz vignettes: vignettes/GSEAlm/inst/doc/GSEAlm.pdf vignetteTitles: Linear models in GSEA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSEAlm/inst/doc/GSEAlm.R importsMe: gCMAP Package: GSRI Version: 2.6.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: multicore License: GPL-3 Title: Gene Set Regulation Index Description: The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI). biocViews: Microarray, Transcription, DifferentialExpression, Genetics, Bioinformatics Author: Julian Gehring, Kilian Bartholome, Clemens Kreutz, Jens Timmer Maintainer: Julian Gehring URL: http://julian-gehring.github.com/GSRI/ MD5sum: 833026887975f2a7e7bc834bb4a4b121 source.ver: src/contrib/GSRI_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSRI_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GSRI_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSRI_2.6.0.tgz vignettes: vignettes/GSRI/inst/doc/gsri.pdf vignetteTitles: Introduction to the GSRI package: Estimating Regulatory Effects utilizing the Gene Set Regulation Index hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GSRI/inst/doc/gsri.R Package: GSVA Version: 1.6.6 Depends: R (>= 2.13.0), methods, GSEABase (>= 1.17.4) Imports: methods, BiocGenerics, Biobase, GSEABase Suggests: limma, RColorBrewer, genefilter, mclust, edgeR, GSVAdata Enhances: snow, parallel License: GPL (>= 2) Archs: i386, x64 Title: Gene Set Variation Analysis for microarray and RNA-seq data Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. biocViews: Microarray, Pathways, GeneSetEnrichment Author: Justin Guinney (with contributions from Robert Castelo and Sonja Haenzelmann ) Maintainer: Justin Guinney URL: http://www.sagebase.org MD5sum: cafb387a55ff0ea7929c4c5278f093ce source.ver: src/contrib/GSVA_1.6.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSVA_1.6.6.zip win64.binary.ver: bin/windows64/contrib/2.15/GSVA_1.6.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSVA_1.6.6.tgz vignettes: vignettes/GSVA/inst/doc/GSVA.pdf vignetteTitles: Gene Set Variation Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSVA/inst/doc/GSVA.R Package: Gviz Version: 1.2.1 Depends: R (>= 2.10.0), methods, grid Imports: IRanges (>= 1.13.19), rtracklayer (>= 1.15.5), lattice, RColorBrewer, biomaRt (>= 2.11.0), GenomicRanges (>= 1.7.14), AnnotationDbi (>= 1.17.11), Biobase (>= 2.15.3), BiocGenerics (>= 0.1.4), GenomicFeatures (>= 1.9.7), BSgenome (>= 1.25.1), Biostrings (>= 2.25.1), biovizBase (>= 1.5.7) Suggests: xtable, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 Title: Plotting data and annotation information along genomic coordinates Description: Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. biocViews: Visualization, Microarray Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou> Maintainer: Florian Hahne MD5sum: 24bb5af31cbc4195c274e8bd671c3751 source.ver: src/contrib/Gviz_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/Gviz_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/Gviz_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Gviz_1.2.1.tgz vignettes: vignettes/Gviz/inst/doc/Gviz.pdf, vignettes/Gviz/inst/doc/ucsc1.pdf, vignettes/Gviz/inst/doc/ucsc2.pdf vignetteTitles: Gviz users guide, ucsc1.pdf, ucsc2.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Gviz/inst/doc/Gviz.R dependsOnMe: cummeRbund importsMe: methyAnalysis, PING suggestsMe: gwascat Package: gwascat Version: 1.2.1 Depends: R (>= 2.14.0), methods, IRanges, GenomicRanges, snpStats, graph, BiocGenerics Imports: Biostrings Suggests: DO.db, Gviz, ggbio, rtracklayer Enhances: SNPlocs.Hsapiens.dbSNP.20111119, pd.genomewidesnp.6 License: Artistic-2.0 Title: representing and modeling data in the NHGRI GWAS catalog Description: representing and modeling data in the NHGRI GWAS catalog Author: VJ Carey Maintainer: VJ Carey MD5sum: dbf9b89bf9f80086ba7c48fd6be0388b source.ver: src/contrib/gwascat_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/gwascat_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/gwascat_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gwascat_1.2.1.tgz vignettes: vignettes/gwascat/inst/doc/gwascat.pdf vignetteTitles: gwascat -- exploring NHGRI GWAS catalog hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gwascat/inst/doc/gwascat.R Package: GWASTools Version: 1.4.2 Depends: Biobase, ncdf, GWASExactHW, sandwich, gdsfmt Imports: methods, DBI, RSQLite, DNAcopy, survival, lmtest, quantsmooth Suggests: GWASdata, RUnit, SNPRelate, snpStats, VariantAnnotation License: Artistic-2.0 Title: Tools for Genome Wide Association Studies Description: Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. biocViews: SNP, GeneticVariability, QualityControl, Microarray Author: Stephanie M. Gogarten, Cathy Laurie, Tushar Bhangale, Matthew P. Conomos, Cecelia Laurie, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar Maintainer: Stephanie M. Gogarten MD5sum: 1f9a54055d2fae2992905f8fdb8d32ea source.ver: src/contrib/GWASTools_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/GWASTools_1.4.2.zip win64.binary.ver: bin/windows64/contrib/2.15/GWASTools_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GWASTools_1.4.2.tgz vignettes: vignettes/GWASTools/inst/doc/Affymetrix.pdf, vignettes/GWASTools/inst/doc/DataCleaning.pdf, vignettes/GWASTools/inst/doc/Formats.pdf, vignettes/GWASTools/inst/doc/VCF.pdf vignetteTitles: Preparing Affymetrix Data, GWAS Data Cleaning, Data formats in GWASTools, Converting VCF data for use in GWASTools hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GWASTools/inst/doc/Affymetrix.R, vignettes/GWASTools/inst/doc/DataCleaning.R, vignettes/GWASTools/inst/doc/Formats.R, vignettes/GWASTools/inst/doc/VCF.R Package: hapFabia Version: 1.0.6 Depends: R (>= 2.12.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils, KernSmooth License: LGPL (>= 2.1) Archs: i386, x64 Title: hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data Description: A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats. biocViews: Genetics, GeneticVariability, SNP, Sequencing, HighThroughputSequencing, Visualization, Clustering, SequenceMatching, Homo_sapiens, Software Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/hapFabia/hapFabia.html MD5sum: 8a078f2aa5f82b2f2bde86c338289f82 source.ver: src/contrib/hapFabia_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/hapFabia_1.0.6.zip win64.binary.ver: bin/windows64/contrib/2.15/hapFabia_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hapFabia_1.0.6.tgz vignettes: vignettes/hapFabia/inst/doc/hapfabia.pdf vignetteTitles: hapFabia: Manual for the R package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hapFabia/inst/doc/hapfabia.R Package: Harshlight Version: 1.30.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: A "corrective make-up" program for microarray chips Description: The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem. biocViews: Microarray, QualityControl, Preprocessing, AffymetrixChip, ReportWriting Author: Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco Maintainer: Maurizio Pellegrino URL: http://asterion.rockefeller.edu/Harshlight/ MD5sum: 880e4c22d5297bc3782535c320c20838 source.ver: src/contrib/Harshlight_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Harshlight_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Harshlight_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Harshlight_1.30.0.tgz vignettes: vignettes/Harshlight/inst/doc/Harshlight.pdf vignetteTitles: Harshlight hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Harshlight/inst/doc/Harshlight.R Package: Heatplus Version: 2.4.0 Imports: graphics, grDevices, stats Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) Title: Heatmaps with row and/or column covariates and colored clusters Description: Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot. biocViews: Microarray, Visualization Author: Alexander Ploner Maintainer: Alexander Ploner MD5sum: c71428fe38f6fa181635704c305935b6 source.ver: src/contrib/Heatplus_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Heatplus_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Heatplus_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Heatplus_2.4.0.tgz vignettes: vignettes/Heatplus/inst/doc/annHeatmapCommentedSource.pdf, vignettes/Heatplus/inst/doc/annHeatmap.pdf, vignettes/Heatplus/inst/doc/oldHeatplus.pdf vignetteTitles: Commented package source, Annotated and regular heatmaps, Old functions (deprecated) hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Heatplus/inst/doc/annHeatmapCommentedSource.R, vignettes/Heatplus/inst/doc/annHeatmap.R, vignettes/Heatplus/inst/doc/oldHeatplus.R dependsOnMe: GeneAnswers, phenoTest Package: HELP Version: 1.16.1 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) Title: Tools for HELP data analysis Description: The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications biocViews: CpGIsland, DNAMethylation, Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, Visualization Author: Reid F. Thompson , John M. Greally , with contributions from Mark Reimers Maintainer: Reid F. Thompson MD5sum: 2bc77c138616f52637bd08719b33462d source.ver: src/contrib/HELP_1.16.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/HELP_1.16.1.zip win64.binary.ver: bin/windows64/contrib/2.15/HELP_1.16.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HELP_1.16.1.tgz vignettes: vignettes/HELP/inst/doc/HELP.pdf vignetteTitles: 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HELP/inst/doc/HELP.R Package: HEM Version: 1.30.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: Heterogeneous error model for identification of differentially expressed genes under multiple conditions Description: This package fits heterogeneous error models for analysis of microarray data biocViews: Microarray, DifferentialExpression, Bioinformatics Author: HyungJun Cho and Jae K. Lee Maintainer: HyungJun Cho URL: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ MD5sum: 8724bedcde18ebcda3ddd94dd05fe7e1 source.ver: src/contrib/HEM_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HEM_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HEM_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HEM_1.30.0.tgz vignettes: vignettes/HEM/inst/doc/HEM.pdf vignetteTitles: HEM Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HEM/inst/doc/HEM.R Package: HilbertVis Version: 1.16.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) Archs: i386, x64 Title: Hilbert curve visualization Description: Functions to visualize long vectors of integer data by means of Hilbert curves biocViews: Visualization Author: Simon Anders Maintainer: Simon Anders URL: http://www.ebi.ac.uk/~anders/hilbert MD5sum: c01bec820963ab1678bea22d1e85c41b source.ver: src/contrib/HilbertVis_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HilbertVis_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HilbertVis_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HilbertVis_1.16.0.tgz vignettes: vignettes/HilbertVis/inst/doc/HilbertDisplay_GUI.pdf, vignettes/HilbertVis/inst/doc/HilbertVis.pdf, vignettes/HilbertVis/inst/doc/ThreeChTest.pdf vignetteTitles: HilbertDisplay_GUI.pdf, Visualising very long data vectors with the Hilbert curve, ThreeChTest.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HilbertVis/inst/doc/HilbertVis.R dependsOnMe: HilbertVisGUI importsMe: ChIPseqR Package: HilbertVisGUI Version: 1.16.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) Archs: i386, x64 Title: HilbertVisGUI Description: An interactive tool to visualize long vectors of integer data by means of Hilbert curves biocViews: Visualization Author: Simon Anders Maintainer: Simon Anders URL: http://www.ebi.ac.uk/~anders/hilbert SystemRequirements: gtkmm-2.4 MD5sum: 39eef101ff3b3bd1551087004b7d453e source.ver: src/contrib/HilbertVisGUI_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HilbertVisGUI_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HilbertVisGUI_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HilbertVisGUI_1.16.0.tgz vignettes: vignettes/HilbertVisGUI/inst/doc/HilbertVisGUI.pdf vignetteTitles: See vignette in package HilbertVis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: TRUE hasLICENSE: FALSE Rfiles: vignettes/HilbertVisGUI/inst/doc/HilbertVisGUI.R Package: HiTC Version: 1.2.0 Depends: R (>= 2.10.0), methods, girafe (>= 1.3.1), genomeIntervals (>= 1.7.1), RColorBrewer Imports: methods, Biobase, Biostrings, graphics, grDevices, ShortRead License: Artistic-2.0 Title: High Throughput Chromosome Conformation Capture analysis Description: The HiTC package was developed to explore high-throughput 'C' data such as 5C or Hi-C. biocViews: Sequencing, HighThroughputSequencing Author: Nicolas Servant Maintainer: Nicolas Servant MD5sum: 62fd8b518c55cf7d6f9236745f0efd25 source.ver: src/contrib/HiTC_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HiTC_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HiTC_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HiTC_1.2.0.tgz vignettes: vignettes/HiTC/inst/doc/HiTC.pdf vignetteTitles: Hight-Throughput Chromosome Conformation Capture analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiTC/inst/doc/HiTC.R Package: HMMcopy Version: 1.0.0 Depends: R (>= 2.10.0), IRanges (>= 1.4.16), geneplotter (>= 1.24.0) License: GPL-3 Archs: i386, x64 Title: Copy number prediction with correction for GC and mappability bias for HTS data Description: Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples. biocViews: Sequencing, Preprocessing, Visualization, CopyNumberVariants, HighThroughputSequencing, Microarray Author: Daniel Lai, Gavin Ha, Sohrab Shah Maintainer: Daniel Lai , Gavin Ha , Sohrab Shah MD5sum: d1c03c527febbfce6ec31815954042f5 source.ver: src/contrib/HMMcopy_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HMMcopy_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HMMcopy_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HMMcopy_1.0.0.tgz vignettes: vignettes/HMMcopy/inst/doc/HMMcopy.pdf vignetteTitles: HMMcopy hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HMMcopy/inst/doc/HMMcopy.R Package: hopach Version: 2.18.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: Biobase, cluster, graphics, grDevices, methods, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) Description: The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). biocViews: Clustering Author: Katherine S. Pollard, with Mark J. van der Laan and Greg Wall Maintainer: Katherine S. Pollard URL: http://www.stat.berkeley.edu/~laan/, http://docpollard.org/ MD5sum: efcf3b7a3420b6e5c62ab8ec4ea5ab21 source.ver: src/contrib/hopach_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/hopach_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/hopach_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hopach_2.18.0.tgz vignettes: vignettes/hopach/inst/doc/bootplot.pdf, vignettes/hopach/inst/doc/dplot.pdf, vignettes/hopach/inst/doc/hopachManuscript.pdf, vignettes/hopach/inst/doc/hopach.pdf, vignettes/hopach/inst/doc/MSS.pdf vignetteTitles: bootplot.pdf, dplot.pdf, hopachManuscript.pdf, hopach, MSS.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hopach/inst/doc/hopach.R importsMe: phenoTest suggestsMe: BiocCaseStudies Package: hpar Version: 1.0.1 Depends: R (>= 2.15) Suggests: org.Hs.eg.db, GO.db, knitr License: Artistic-2.0 Title: Human Protein Atlas in R Description: A simple interface to and data from the Human Protein Atlas project. biocViews: Bioinformatics, Proteomics, Homo_sapiens, CellBiology Author: Laurent Gatto Maintainer: Laurent Gatto MD5sum: c9c7173234320af0fce1849a3343093f source.ver: src/contrib/hpar_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/hpar_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/hpar_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hpar_1.0.1.tgz vignettes: vignettes/hpar/inst/doc/hpar.pdf vignetteTitles: hpar hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hpar/inst/doc/hpar.R Package: HTqPCR Version: 1.12.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 Title: Automated analysis of high-throughput qPCR data Description: Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs). biocViews: MicrotitrePlateAssay, DifferentialExpression, GeneExpression, DataImport, QualityControl, Preprocessing, Bioinformatics, Visualization, MultipleComparisons, qPCR Author: Heidi Dvinge, Paul Bertone Maintainer: Heidi Dvinge URL: http://www.ebi.ac.uk/bertone/software MD5sum: 73c267cc48f72d39f17c899f3edac536 source.ver: src/contrib/HTqPCR_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HTqPCR_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HTqPCR_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HTqPCR_1.12.0.tgz vignettes: vignettes/HTqPCR/inst/doc/HTqPCR.pdf vignetteTitles: qPCR analysis in R hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HTqPCR/inst/doc/HTqPCR.R Package: HTSanalyzeR Version: 2.10.0 Depends: R (>= 2.15), igraph0, methods Imports: graph, igraph0, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt, RankProd Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow License: Artistic-2.0 Title: Gene set over-representation, enrichment and network analyses for high-throughput screens Description: This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. The over-representation analysis is performed based on hypergeometric tests. The enrichment analysis is based on the GSEA algorithm (Subramanian et al. PNAS 2005). The network analysis identifies enriched subnetworks based on algorithms from the BioNet package (Beisser et al., Bioinformatics 2010). A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package. biocViews: CellBasedAssays, Bioinformatics, MultipleComparisons Author: Xin Wang , Camille Terfve , John C. Rose , Florian Markowetz Maintainer: Xin Wang MD5sum: c596c41d5918d48ff962fa95c616be11 source.ver: src/contrib/HTSanalyzeR_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HTSanalyzeR_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HTSanalyzeR_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HTSanalyzeR_2.10.0.tgz vignettes: vignettes/HTSanalyzeR/inst/doc/Figure.pdf, vignettes/HTSanalyzeR/inst/doc/HTSanalyzeR-Vignette.pdf vignetteTitles: Figure.pdf, Main vignette:Gene set enrichment and network analysis of high-throughput RNAi screen data using HTSanalyzeR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HTSanalyzeR/inst/doc/HTSanalyzeR-Vignette.R importsMe: phenoTest Package: HTSeqGenie Version: 1.0.0 Depends: R (>= 2.15.0), ShortRead (>= 1.14.4), parallel, hwriter, Cairo, tools, gmapR (>= 0.99.23), logging Imports: BiocGenerics (>= 0.2.0), IRanges (>= 1.14.3), GenomicRanges (>= 1.7.12), Rsamtools (>= 1.8.5), Biostrings (>= 2.24.1), chipseq (>= 1.7.1), rtracklayer (>= 1.17.19), GenomicFeatures (>= 1.9.31) Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, GenomicFeatures, LungCancerLines, org.Hs.eg.db License: Artistic-2.0 Title: High-throughput sequencing data analysis pipeline. Description: A software package to analyse high-throughput sequencing experiments Author: Gregoire Pau, Cory Barr, Jens Reeder, Michael Lawrence, Jeremiah Degenhardt, Tom Wu, Melanie Huntley, Matt Brauer Maintainer: Gregoire Pau MD5sum: 6fa594d206683ba5de58b55c2d20e5c9 source.ver: src/contrib/HTSeqGenie_1.0.0.tar.gz vignettes: vignettes/HTSeqGenie/inst/doc/HTSeqGenie.pdf vignetteTitles: gmapR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HTSeqGenie/inst/doc/HTSeqGenie.R Package: htSeqTools Version: 1.4.0 Depends: R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase, IRanges, methods, MASS, BSgenome, GenomicRanges Enhances: multicore License: GPL (>=2) Title: Quality Control, Visualization and Processing for High-Throughput Sequencing data Description: We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles. biocViews: HighThroughputSequencing,QualityControl Author: Evarist Planet, Camille Stephan-Otto, Oscar Reina, Oscar Flores, David Rossell Maintainer: Oscar Reina MD5sum: b6f26207649b369167875c0ea727fa94 source.ver: src/contrib/htSeqTools_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/htSeqTools_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/htSeqTools_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/htSeqTools_1.4.0.tgz vignettes: vignettes/htSeqTools/inst/doc/htSeqTools.pdf vignetteTitles: Manual for the htSeqTools library hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/htSeqTools/inst/doc/htSeqTools.R Package: HybridMTest Version: 1.2.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL Version 2 or later Title: Hybrid Multiple Testing Description: Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs. biocViews: GeneExpression, Genetics, Bioinformatics, Microarray Author: Stan Pounds , Demba Fofana Maintainer: Demba Fofana MD5sum: 45a9cbf37e9a80c8aff4f1730115e07d source.ver: src/contrib/HybridMTest_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HybridMTest_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HybridMTest_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HybridMTest_1.2.0.tgz vignettes: vignettes/HybridMTest/inst/doc/HybridMTest.pdf vignetteTitles: Hybrid Multiple Testing hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HybridMTest/inst/doc/HybridMTest.R Package: hyperdraw Version: 1.10.0 Depends: R (>= 2.9.0), methods, grid, graph, hypergraph, Rgraphviz Imports: stats4 License: GPL (>= 2) Title: Visualizing Hypergaphs Description: Functions for visualizing hypergraphs. biocViews: NetworkVisualization, GraphsAndNetworks Author: Paul Murrell Maintainer: Paul Murrell SystemRequirements: graphviz MD5sum: b393a59e32a2d7d5def3dff627fd503f source.ver: src/contrib/hyperdraw_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/hyperdraw_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/hyperdraw_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hyperdraw_1.10.0.tgz vignettes: vignettes/hyperdraw/inst/doc/hyperdraw.pdf vignetteTitles: Hyperdraw hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hyperdraw/inst/doc/hyperdraw.R Package: hypergraph Version: 1.30.0 Depends: R (>= 2.1.0), methods, graph License: Artistic-2.0 Title: A package providing hypergraph data structures Description: A package that implements some simple capabilities for representing and manipulating hypergraphs. biocViews: GraphsAndNetworks Author: Seth Falcon, Robert Gentleman Maintainer: Bioconductor Package Maintainer MD5sum: b2aa1392197faa55049c4e8adb4d93ee source.ver: src/contrib/hypergraph_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/hypergraph_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/hypergraph_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hypergraph_1.30.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: altcdfenvs, hyperdraw, RpsiXML Package: iASeq Version: 1.2.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 Title: iASeq: integrating multiple sequencing datasets for detecting allele-specific events Description: It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies. biocViews: SNP, RNAseq, ChIPseq, Bioinformatics Author: Yingying Wei, Hongkai Ji Maintainer: Yingying Wei MD5sum: 5d57c79e8cdd710e5070fbb6d9fe418e source.ver: src/contrib/iASeq_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iASeq_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iASeq_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iASeq_1.2.0.tgz vignettes: vignettes/iASeq/inst/doc/iASeqVignette.pdf vignetteTitles: iASeq Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iASeq/inst/doc/iASeqVignette.R Package: iBBiG Version: 1.2.0 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 Archs: i386, x64 Title: Iterative Binary Biclustering of Genesets Description: iBBiG is a bi-clustering algorithm which is optimizes for binary data analysis. We apply it to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. iBBiG does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes biocViews: Clustering, Annotation, GeneSetEnrichment Author: Daniel Gusenleitner, Aedin Culhane Maintainer: Aedin Culhane URL: http://bcb.dfci.harvard.edu/~aedin/publications/ MD5sum: a78d604d83623d6f08839fa31e5c7e7c source.ver: src/contrib/iBBiG_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iBBiG_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iBBiG_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iBBiG_1.2.0.tgz vignettes: vignettes/iBBiG/inst/doc/tutorial.pdf vignetteTitles: iBBiG User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iBBiG/inst/doc/tutorial.R Package: ibh Version: 1.6.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) Title: Interaction Based Homogeneity for Evaluating Gene Lists Description: This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions. biocViews: QualityControl, DataImport, GraphsAndNetworks, NetworkEnrichment Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin Atalay. Maintainer: Kircicegi Korkmaz MD5sum: 494a7908468f187b804f18c95977b2ba source.ver: src/contrib/ibh_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ibh_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ibh_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ibh_1.6.0.tgz vignettes: vignettes/ibh/inst/doc/ibh.pdf vignetteTitles: ibh hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ibh/inst/doc/ibh.R Package: Icens Version: 1.30.0 Depends: survival Imports: graphics License: Artistic-2.0 Title: NPMLE for Censored and Truncated Data Description: Many functions for computing the NPMLE for censored and truncated data. biocViews: Bioinformatics, Infrastructure Author: R. Gentleman and Alain Vandal Maintainer: Bioconductor Package Maintainer MD5sum: ac1ce285046dd473fef924bab9f2d1e6 source.ver: src/contrib/Icens_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Icens_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Icens_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Icens_1.30.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PROcess importsMe: PROcess Package: iChip Version: 1.12.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models Description: This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates. biocViews: ChIPchip, NimbleGen, Affymetrix, Agilent,Microarray, Bioinformatics Author: Qianxing Mo Maintainer: Qianxing Mo MD5sum: b0bc7730ffd848f3a54de85cdb048d96 source.ver: src/contrib/iChip_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iChip_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iChip_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iChip_1.12.0.tgz vignettes: vignettes/iChip/inst/doc/iChip.pdf vignetteTitles: iChip hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iChip/inst/doc/iChip.R Package: idiogram Version: 1.34.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 Title: idiogram Description: A package for plotting genomic data by chromosomal location biocViews: Visualization Author: Karl J. Dykema Maintainer: Karl J. Dykema MD5sum: 5356025a6c22d553013101b3b14b2e14 source.ver: src/contrib/idiogram_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/idiogram_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/idiogram_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/idiogram_1.34.0.tgz vignettes: vignettes/idiogram/inst/doc/idiogram.pdf vignetteTitles: HOWTO: idiogram hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/idiogram/inst/doc/idiogram.R dependsOnMe: reb Package: IdMappingAnalysis Version: 1.2.1 Depends: R (>= 2.14), R.oo (>= 1.10.1), rChoiceDialogs Imports: boot, mclust, RColorBrewer, Biobase License: GPL-2 Title: ID Mapping Analysis Description: Identifier mapping performance analysis biocViews: Bioinformatics, Annotation, MultipleComparisons Author: Alex Lisovich, Roger Day Maintainer: Alex Lisovich , Roger Day MD5sum: 847750c422f160cbc38941c9c23594e7 source.ver: src/contrib/IdMappingAnalysis_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/IdMappingAnalysis_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/IdMappingAnalysis_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IdMappingAnalysis_1.2.1.tgz vignettes: vignettes/IdMappingAnalysis/inst/doc/IdMappingAnalysis.pdf vignetteTitles: Critically comparing identifier maps retrieved from bioinformatics annotation resources. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/IdMappingAnalysis/inst/doc/IdMappingAnalysis.R Package: IdMappingRetrieval Version: 1.4.0 Depends: R.oo, XML, RCurl, rChoiceDialogs, ENVISIONQuery Imports: biomaRt, ENVISIONQuery, DAVIDQuery, AffyCompatible, R.methodsS3, R.oo, utils License: GPL-2 Title: ID Mapping Data Retrieval Description: Data retrieval for identifier mapping performance analysis biocViews: Bioinformatics, Annotation, MultipleComparisons Author: Alex Lisovich, Roger Day Maintainer: Alex Lisovich , Roger Day MD5sum: 395bb70d48a75ddecd1338e23d8832d9 source.ver: src/contrib/IdMappingRetrieval_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/IdMappingRetrieval_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/IdMappingRetrieval_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IdMappingRetrieval_1.4.0.tgz vignettes: vignettes/IdMappingRetrieval/inst/doc/IdMappingRetrieval.pdf vignetteTitles: Collection and subsequent fast retrieval of identifier mapping related information from various online sources. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/IdMappingRetrieval/inst/doc/IdMappingRetrieval.R Package: iFlow Version: 2.10.0 Depends: R (>= 2.13.0), flowCore, flowViz, flowStats (>= 1.3.20) Imports: Biobase, RGtk2, cairoDevice, flowCore, flowStats, flowViz, grDevices, graphics, methods, utils License: Artistic-2.0 Title: GUI based visualization for flow cytometry Description: Tool to explore and visualize flow cytometry biocViews: FlowCytometry, Bioinformatics, GUI Author: Kyongryun Lee, Florian Hahne, Deepayan Sarkar Maintainer: Kyongryun Lee URL: http://www.hindawi.com/journals/abi/2009/103839.html MD5sum: 96122598272bbf583a3facadecd6825b source.ver: src/contrib/iFlow_2.10.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iFlow_2.10.0.tgz vignettes: vignettes/iFlow/inst/doc/iflow.pdf vignetteTitles: How to iFlow hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iFlow/inst/doc/iflow.R Package: imageHTS Version: 1.8.0 Depends: R (>= 2.9.0), EBImage (>= 3.99.17), cellHTS2 (>= 2.10.0) Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071 Suggests: MASS License: LGPL-2.1 Title: Analysis of high-throughput microscopy-based screens Description: imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopy-based datasets. biocViews: CellBasedAssays, Visualization, Preprocessing Author: Gregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber Maintainer: Gregoire Pau MD5sum: fdf7b446e023edca4561cca3d1918340 source.ver: src/contrib/imageHTS_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/imageHTS_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/imageHTS_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/imageHTS_1.8.0.tgz vignettes: vignettes/imageHTS/inst/doc/imageHTS-introduction.pdf vignetteTitles: Analysis of high-throughput microscopy-based screens with imageHTS hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/imageHTS/inst/doc/imageHTS-introduction.R dependsOnMe: phenoDist Package: impute Version: 1.32.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Title: impute: Imputation for microarray data Description: Imputation for microarray data (currently KNN only) biocViews: Bioinformatics, Microarray Author: Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu Maintainer: Balasubramanian Narasimhan MD5sum: 0964c072590885b349bc68dc295497ee source.ver: src/contrib/impute_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/impute_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/impute_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/impute_1.32.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet Package: inSilicoDb Version: 1.7.4 Depends: R (>= 2.11.0), rjson, Biobase Imports: RCurl Suggests: limma License: GPL-2 Title: Access to the InSilico Database Description: Access Human Affymetrix expert curated Gene Expression Omnibus (GEO) datasets from the InSilico Database. biocViews: Microarray, DataImport Author: Jonatan Taminau Maintainer: Jonatan Taminau , David Steenhoff URL: https://insilicodb.org MD5sum: 513b496fdb6f09d87a8ab80e2dbbeba2 source.ver: src/contrib/inSilicoDb_1.7.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/inSilicoDb_1.7.4.zip win64.binary.ver: bin/windows64/contrib/2.15/inSilicoDb_1.7.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/inSilicoDb_1.7.4.tgz vignettes: vignettes/inSilicoDb/inst/doc/inSilicoDb.pdf vignetteTitles: Using the inSilicoDb package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/inSilicoDb/inst/doc/inSilicoDb.R suggestsMe: inSilicoMerging Package: inSilicoMerging Version: 1.2.3 Depends: R (>= 2.11.1), Biobase, DWD, limma Imports: amap, moments Suggests: BiocGenerics, inSilicoDb License: GPL-2 Title: Collection of Merging Techniques for Gene Expression Data Description: Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies. biocViews: Microarray Author: Jonatan Taminau , Stijn Meganck , Cosmin Lazar Maintainer: Jonatan Taminau , Stijn Meganck , Cosmin Lazar URL: https://insilicodb.org/ MD5sum: 3ad0e3cc74013174a43011da5c2d8ec0 source.ver: src/contrib/inSilicoMerging_1.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/inSilicoMerging_1.2.3.zip win64.binary.ver: bin/windows64/contrib/2.15/inSilicoMerging_1.2.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/inSilicoMerging_1.2.3.tgz vignettes: vignettes/inSilicoMerging/inst/doc/inSilicoMerging.pdf vignetteTitles: Using the inSilicoMerging package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/inSilicoMerging/inst/doc/inSilicoMerging.R Package: inveRsion Version: 1.6.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) Archs: i386, x64 Title: Inversions in genotype data Description: Package to find genetic inversions in genotype (SNP array) data. biocViews: Microarray, SNP Author: Alejandro Caceres Maintainer: Alejandro Caceres MD5sum: 9feb21f975d085c4dc21be655b71dbca source.ver: src/contrib/inveRsion_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/inveRsion_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/inveRsion_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/inveRsion_1.6.0.tgz vignettes: vignettes/inveRsion/inst/doc/inveRsion.pdf, vignettes/inveRsion/inst/doc/Manual.pdf vignetteTitles: Quick start guide for inveRsion package, Manual.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/inveRsion/inst/doc/inveRsion.R Package: iontree Version: 1.4.0 Depends: methods, rJava, RSQLite, XML Suggests: iontreeData License: GPL-2 Title: Data management and analysis of ion trees from ion-trap mass spectrometry Description: Ion fragmentation provides structural information for metabolite identification. This package provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. biocViews: Metabolomics, MassSpectrometry Author: Mingshu Cao Maintainer: Mingshu Cao MD5sum: 618ff3a2fc6f620efeed7d742164c71a source.ver: src/contrib/iontree_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iontree_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iontree_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iontree_1.4.0.tgz vignettes: vignettes/iontree/inst/doc/iontree_doc.pdf vignetteTitles: MSn hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/iontree/inst/doc/iontree_doc.R Package: iPAC Version: 1.0.0 Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest License: GPL-2 Title: Identification of Protein Amino acid Clustering Description: iPAC is a novel tool to identify somatic amino acid mutation clustering within proteins while taking into account protein structure. biocViews: Bioinformatics, Clustering, BiologicalDomains, Proteomics Author: Gregory Ryslik, Hongyu Zhao Maintainer: Gregory Ryslik MD5sum: 64df228a3e89bdf1a2038d3e10ac873e source.ver: src/contrib/iPAC_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iPAC_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iPAC_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iPAC_1.0.0.tgz vignettes: vignettes/iPAC/inst/doc/iPAC.pdf vignetteTitles: iPAC: identification of Protein Amino acid Mutations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iPAC/inst/doc/iPAC.R Package: IPPD Version: 1.6.0 Depends: R (>= 2.12.0), MASS, Matrix, XML, digest, bitops Imports: methods, stats, graphics License: GPL (version 2 or later) Archs: i386, x64 Title: Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching Description: The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs. biocViews: Proteomics Author: Martin Slawski , Rene Hussong , Matthias Hein Maintainer: Martin Slawski MD5sum: a44e1694684e996bbdca54ec6bb8a9b0 source.ver: src/contrib/IPPD_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/IPPD_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/IPPD_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IPPD_1.6.0.tgz vignettes: vignettes/IPPD/inst/doc/IPPD.pdf, vignettes/IPPD/inst/doc/templatedetail.pdf, vignettes/IPPD/inst/doc/templates.pdf vignetteTitles: IPPD Manual, templatedetail.pdf, templates.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/IPPD/inst/doc/IPPD.R Package: IRanges Version: 1.16.6 Depends: R (>= 2.8.0), methods, utils, stats, BiocGenerics (>= 0.1.4) Imports: methods, utils, stats, BiocGenerics, stats4 Suggests: GenomicRanges, RUnit License: Artistic-2.0 Archs: i386, x64 Title: Infrastructure for manipulating intervals on sequences Description: The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible. biocViews: Infrastructure, DataRepresentation Author: H. Pages, P. Aboyoun and M. Lawrence Maintainer: Bioconductor Package Maintainer MD5sum: cb350d44ff25896567b127e3d02b7e36 source.ver: src/contrib/IRanges_1.16.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/IRanges_1.16.6.zip win64.binary.ver: bin/windows64/contrib/2.15/IRanges_1.16.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IRanges_1.16.6.tgz vignettes: vignettes/IRanges/inst/doc/IRangesOverview.pdf, vignettes/IRanges/inst/doc/RleTricks.pdf vignetteTitles: An Introduction to IRanges, Rle Tips and Tricks hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/IRanges/inst/doc/IRangesOverview.R, vignettes/IRanges/inst/doc/RleTricks.R dependsOnMe: BayesPeak, Biostrings, BSgenome, bsseq, ChIPpeakAnno, chipseq, chroGPS, cn.mops, CSAR, DECIPHER, deepSNV, DirichletMultinomial, easyRNASeq, exomeCopy, genomes, GenomicFeatures, GenomicRanges, Genominator, genoset, GGtools, girafe, gwascat, HMMcopy, htSeqTools, methyAnalysis, MinimumDistance, MotifDb, nucleR, oneChannelGUI, PING, r3Cseq, rGADEM, rMAT, Rsamtools, segmentSeq, ShortRead, TEQC, triform, VariantAnnotation, VariantTools, xmapcore importsMe: annmap, AnnotationDbi, ArrayExpressHTS, BayesPeak, Biostrings, biovizBase, BitSeq, charm, ChIPpeakAnno, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, cn.mops, DECIPHER, DiffBind, EDASeq, fastseg, flowQ, FunciSNP, gcrma, GenomicFeatures, GenomicRanges, ggbio, girafe, gmapR, Gviz, HTSeqGenie, MEDIPS, methVisual, methyAnalysis, mosaics, motifRG, MotIV, MSnbase, NarrowPeaks, nucleR, oligoClasses, OTUbase, pdInfoBuilder, PICS, R453Plus1Toolbox, Rcade, REDseq, Repitools, rGADEM, rMAT, rnaSeqMap, Rolexa, Rsamtools, rSFFreader, rtracklayer, segmentSeq, ShortRead, triform, TSSi, VanillaICE, VariantAnnotation, VariantTools, waveTiling suggestsMe: BiocGenerics, HilbertVis, HilbertVisGUI, MiRaGE, Repitools, SNPchip Package: iSeq Version: 1.10.0 Depends: R (>= 2.10.0) License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models Description: This package uses Bayesian hidden Ising models to identify IP-enriched genomic regions from ChIP-seq data. It can be used to analyze ChIP-seq data with and without controls and replicates. biocViews: ChIPseq, HighThroughputSequencing, Bioinformatics Author: Qianxing Mo Maintainer: Qianxing Mo MD5sum: 741ab42e8c9d3e4da1e90413f66e3111 source.ver: src/contrib/iSeq_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iSeq_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iSeq_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iSeq_1.10.0.tgz vignettes: vignettes/iSeq/inst/doc/iSeq.pdf vignetteTitles: iSeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iSeq/inst/doc/iSeq.R Package: isobar Version: 1.4.0 Depends: R (>= 2.10.0), Biobase, stats, methods, plyr Imports: distr Suggests: MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2, Hmisc, RJSONIO License: LGPL-2 Title: Analysis and quantitation of isobarically tagged MSMS proteomics data Description: isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. biocViews: Proteomics, MassSpectrometry, Bioinformatics, MultipleComparisons, QualityControl Author: Florian P Breitwieser and Jacques Colinge , with contributions from Xavier Robin Maintainer: Florian P Breitwieser URL: http://bioinformatics.cemm.oeaw.ac.at MD5sum: c2afab27ab6bb80e0044efb486432480 source.ver: src/contrib/isobar_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/isobar_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/isobar_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/isobar_1.4.0.tgz vignettes: vignettes/isobar/inst/doc/isobar-devel.pdf, vignettes/isobar/inst/doc/isobar.pdf vignetteTitles: Isobar for developers, Isobar Usage hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/isobar/inst/doc/isobar-devel.R, vignettes/isobar/inst/doc/isobar.R Package: IsoGeneGUI Version: 1.14.0 Depends: tcltk, tkrplot, IsoGene Imports: multtest, relimp, WriteXLS,gdata, RColorBrewer, geneplotter Suggests: RUnit License: GPL-2 Title: A graphical user interface to conduct a dose-response analysis of microarray data Description: The IsoGene Graphical User Interface (IsoGene-GUI) is a user friendly interface of the IsoGene package which is aimed to identify for genes with a monotonic trend in the expression levels with respect to the increasing doses using several test statistics: global likelihood ratio test (E2), Bartholomew 1961, Barlow et al. 1972 and Robertson et al. 1988), Williams (1971, 1972), Marcus (1976), the M (Hu et al. 2005) and the modified M (Lin et al. 2007). The p-values of the global likelihood ratio test (E2) are obtained using the excat distribution and permutation. The other four test statistics are obtained using permutation . Several p-values adjustment are provided: Bonferroni, Holm (1979), Hochberg (1988), and Sidak procedures for controlling the family-wise Type I error rate (FWER), and BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2001) procedures are used for controlling the FDR. the inference is based on resampling methods, which control the False Discovery Rate (FDR) (both permutations (Ge et al., 2003) and the Significance Analysis of Microarrays (SAM), Tusher et al., 2001). biocViews: Microarray, DifferentialExpression, GUI Author: Setia Pramana, Dan Lin, Philippe Haldermans, Tobias Verbeke Maintainer: Setia Pramana URL: http://www.ibiostat.be/software/IsoGeneGUI/index.html MD5sum: f99f837c4a0c80f05565600b6e464eee source.ver: src/contrib/IsoGeneGUI_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/IsoGeneGUI_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/IsoGeneGUI_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IsoGeneGUI_1.14.0.tgz vignettes: vignettes/IsoGeneGUI/inst/doc/IsoGeneGUI.pdf vignetteTitles: IsoGeneGUI Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/IsoGeneGUI/inst/doc/IsoGeneGUI.R Package: ITALICS Version: 2.18.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 Title: ITALICS Description: A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set biocViews: Microarray, CopyNumberVariants Author: Guillem Rigaill, Philippe Hupe Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr MD5sum: 010a14d39f7b2764a2926b283b8ece8d source.ver: src/contrib/ITALICS_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ITALICS_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ITALICS_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ITALICS_2.18.0.tgz vignettes: vignettes/ITALICS/inst/doc/ITALICS-006.pdf, vignettes/ITALICS/inst/doc/ITALICS.pdf vignetteTitles: ITALICS-006.pdf, ITALICS hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ITALICS/inst/doc/ITALICS.R Package: iterativeBMA Version: 1.16.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) Title: The Iterative Bayesian Model Averaging (BMA) algorithm Description: The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402). biocViews: Microarray, Bioinformatics, Classification Author: Ka Yee Yeung, University of Washington, Seattle, WA, with contributions from Adrian Raftery and Ian Painter Maintainer: Ka Yee Yeung URL: http://faculty.washington.edu/kayee/research.html MD5sum: 0afd20fa6e09a5bee3fecba33c7718a6 source.ver: src/contrib/iterativeBMA_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iterativeBMA_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iterativeBMA_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iterativeBMA_1.16.0.tgz vignettes: vignettes/iterativeBMA/inst/doc/iterativeBMA.pdf vignetteTitles: The Iterative Bayesian Model Averaging Algorithm hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iterativeBMA/inst/doc/iterativeBMA.R Package: iterativeBMAsurv Version: 1.16.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) Title: The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis Description: The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data. biocViews: Microarray, Bioinformatics Author: Amalia Annest, University of Washington, Tacoma, WA Ka Yee Yeung, University of Washington, Seattle, WA Maintainer: Ka Yee Yeung URL: http://expression.washington.edu/ibmasurv/protected MD5sum: b73f372f396853862b31deb07e7152d0 source.ver: src/contrib/iterativeBMAsurv_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iterativeBMAsurv_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iterativeBMAsurv_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iterativeBMAsurv_1.16.0.tgz vignettes: vignettes/iterativeBMAsurv/inst/doc/iterativeBMAsurv.pdf vignetteTitles: The Iterative Bayesian Model Averaging Algorithm For Survival Analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iterativeBMAsurv/inst/doc/iterativeBMAsurv.R Package: joda Version: 1.6.0 Depends: R (>= 2.0), bgmm, RBGL License: GPL (>= 2) Title: JODA algorithm for quantifying gene deregulation using knowledge Description: Package 'joda' implements three steps of an algorithm called JODA. The algorithm computes gene deregulation scores. For each gene, its deregulation score reflects how strongly an effect of a certain regulator's perturbation on this gene differs between two different cell populations. The algorithm utilizes regulator knockdown expression data as well as knowledge about signaling pathways in which the regulators are involved (formalized in a simple matrix model). biocViews: Microarray, Pathways, GraphsAndNetworks, Statistics, NetworkInference Author: Ewa Szczurek Maintainer: Ewa Szczurek URL: http://www.bioconductor.org MD5sum: 25b170ce4a4a3d2dd369caa6ee9e892e source.ver: src/contrib/joda_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/joda_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/joda_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/joda_1.6.0.tgz vignettes: vignettes/joda/inst/doc/JodaVignette.pdf vignetteTitles: Introduction to joda hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/joda/inst/doc/JodaVignette.R Package: KCsmart Version: 2.16.0 Depends: methods, siggenes, multtest, KernSmooth Enhances: Biobase, CGHbase License: GPL-3 Title: Multi sample aCGH analysis package using kernel convolution Description: Multi sample aCGH analysis package using kernel convolution biocViews: CopyNumberVariants, Visualization, aCGH, Microarray Author: Jorma de Ronde, Christiaan Klijn, Arno Velds Maintainer: Jorma de Ronde MD5sum: c74f2d0234ab4c75f3e51d02f415e1f1 source.ver: src/contrib/KCsmart_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/KCsmart_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/KCsmart_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/KCsmart_2.16.0.tgz vignettes: vignettes/KCsmart/inst/doc/KCS.pdf vignetteTitles: KCsmart example session hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KCsmart/inst/doc/KCS.R Package: KEGGgraph Version: 1.14.0 Depends: R (>= 2.10), methods, XML (>= 2.3-0), graph Imports: methods, XML, graph Suggests: Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) Title: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor Description: KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc. biocViews: Pathways, GraphsAndNetworks, NetworkVisualization Author: Jitao David Zhang Maintainer: Jitao David Zhang URL: http://www.nextbiomotif.com MD5sum: 7fad1b40037731dd38b1f8b9a51fee3d source.ver: src/contrib/KEGGgraph_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/KEGGgraph_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/KEGGgraph_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/KEGGgraph_1.14.0.tgz vignettes: vignettes/KEGGgraph/inst/doc/KEGGgraphApp.pdf, vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf vignetteTitles: KEGGgraph: Application Examples, KEGGgraph: graph approach to KEGG PATHWAY hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KEGGgraph/inst/doc/KEGGgraphApp.R, vignettes/KEGGgraph/inst/doc/KEGGgraph.R importsMe: DEGraph, NCIgraph suggestsMe: DEGraph, SPIA Package: keggorthology Version: 2.10.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 Title: graph support for KO, KEGG Orthology Description: graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs. biocViews: Pathways, GraphsAndNetworks, NetworkVisualization Author: VJ Carey Maintainer: VJ Carey MD5sum: 62a2082d257b4a5477992df3f18b4580 source.ver: src/contrib/keggorthology_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/keggorthology_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/keggorthology_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/keggorthology_2.10.0.tgz vignettes: vignettes/keggorthology/inst/doc/keggorth.pdf vignetteTitles: keggorthology overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/keggorthology/inst/doc/keggorth.R dependsOnMe: gene2pathway suggestsMe: MLInterfaces Package: KEGGprofile Version: 1.0.0 Depends: XML, png, TeachingDemos, KEGG.db Imports: AnnotationDbi License: GPL (>= 2) Title: An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway Description: KEGGprofile is an annotation and visualization tool which integrated the expression profiles and the function annotation in KEGG pathway maps. The multi-types and multi-groups expression data can be visualized in one pathway map. KEGGprofile facilitated more detailed analysis about the specific function changes inner pathway or temporal correlations in different genes and samples. biocViews: Pathways Author: Shilin Zhao Maintainer: Shilin Zhao MD5sum: 1fc59a59c4fa1dec4b375399fa1bc86e source.ver: src/contrib/KEGGprofile_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/KEGGprofile_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/KEGGprofile_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/KEGGprofile_1.0.0.tgz vignettes: vignettes/KEGGprofile/inst/doc/KEGGprofile.pdf vignetteTitles: KEGGprofile: Application Examples hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KEGGprofile/inst/doc/KEGGprofile.R Package: KEGGSOAP Version: 1.32.1 Depends: methods, BiocGenerics Imports: XML, RCurl, SSOAP (>= 0.2-2), XMLSchema Suggests: RUnit License: BSD Title: Client-side SOAP access KEGG Description: A package that provides a client interface to the KEGG SOAP server biocViews: Annotation, Pathways, ConnectTools Author: J. Zhang and R. Gentleman Maintainer: Bioconductor Package Maintainer MD5sum: d609596ea0c04ca66087c133d1bdfaf7 source.ver: src/contrib/KEGGSOAP_1.32.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/KEGGSOAP_1.32.1.zip win64.binary.ver: bin/windows64/contrib/2.15/KEGGSOAP_1.32.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/KEGGSOAP_1.32.1.tgz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: gene2pathway Package: lapmix Version: 1.24.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) Title: Laplace Mixture Model in Microarray Experiments Description: Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes. biocViews: Bioinformatics, Microarray, OneChannel, DifferentialExpression Author: Yann Ruffieux, contributions from Debjani Bhowmick, Anthony C. Davison, and Darlene R. Goldstein Maintainer: Yann Ruffieux URL: http://www.r-project.org, http://www.bioconductor.org, http://stat.epfl.ch MD5sum: dea2902dd6d9348df61d812ca3fca5ad source.ver: src/contrib/lapmix_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/lapmix_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/lapmix_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lapmix_1.24.0.tgz vignettes: vignettes/lapmix/inst/doc/lapmix-example.pdf vignetteTitles: lapmix example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/lapmix/inst/doc/lapmix-example.R Package: LBE Version: 1.26.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue License: GPL-2 Title: Estimation of the false discovery rate. Description: LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. biocViews: Bioinformatics, MultipleComparisons Author: Cyril Dalmasso Maintainer: Cyril Dalmasso MD5sum: 1921ab8b122a05bb93f291e6d9f42c53 source.ver: src/contrib/LBE_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LBE_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LBE_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LBE_1.26.0.tgz vignettes: vignettes/LBE/inst/doc/LBE.pdf vignetteTitles: LBE Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LBE/inst/doc/LBE.R Package: les Version: 1.8.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: multicore License: GPL-3 Title: Identifying Differential Effects in Tiling Microarray Data Description: The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. biocViews: Microarray, Bioinformatics, DifferentialExpression, ChIPchip, DNAMethylation, Transcription Author: Julian Gehring, Clemens Kreutz, Jens Timmer Maintainer: Julian Gehring URL: http://julian-gehring.github.com/les/ MD5sum: 6f6bf27f65dd87fe958bbdd77c502d04 source.ver: src/contrib/les_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/les_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/les_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/les_1.8.0.tgz vignettes: vignettes/les/inst/doc/les.pdf vignetteTitles: Introduction to the les package: Identifying Differential Effects in Tiling Microarray Data with the Loci of Enhanced Significance Framework hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/les/inst/doc/les.R importsMe: GSRI Package: limma Version: 3.14.4 Depends: R (>= 2.3.0), methods Suggests: affy, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn License: GPL (>=2) Archs: i386, x64 Title: Linear Models for Microarray Data Description: Data analysis, linear models and differential expression for microarray data. biocViews: Microarray, OneChannel, TwoChannel, DataImport, QualityControl, Preprocessing, Bioinformatics, DifferentialExpression, MultipleComparisons, TimeCourse Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Davis McCarthy, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang Hu, Wei Shi and Belinda Phipson. Maintainer: Gordon Smyth URL: http://bioinf.wehi.edu.au/limma MD5sum: 1586bf14613a0c080fc0e8ba192dedb6 source.ver: src/contrib/limma_3.14.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/limma_3.14.4.zip win64.binary.ver: bin/windows64/contrib/2.15/limma_3.14.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/limma_3.14.4.tgz vignettes: vignettes/limma/inst/doc/limma.pdf, vignettes/limma/inst/doc/usersguide.pdf vignetteTitles: Limma Vignette, usersguide.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/limma/inst/doc/limma.R htmlDocs: vignettes/limma/inst/doc/index.html dependsOnMe: a4Base, AffyExpress, affylmGUI, Agi4x44PreProcess, attract, birta, CALIB, cghMCR, ChIPpeakAnno, codelink, convert, Cormotif, coRNAi, edgeR, ExiMiR, HTqPCR, inSilicoMerging, limmaGUI, lmdme, maDB, maigesPack, marray, MmPalateMiRNA, nem, PADOG, qpcrNorm, Ringo, snapCGH, TurboNorm importsMe: affycoretools, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, attract, beadarray, betr, CALIB, CancerMutationAnalysis, charm, ChIPpeakAnno, explorase, gCMAP, GeneSelectMMD, GeneSelector, GGBase, HTqPCR, iChip, maSigPro, minfi, MmPalateMiRNA, OLIN, PADOG, phenoTest, Ringo, RNAinteract, RNAither, RTopper, snapCGH, SSPA, timecourse, tweeDEseq, vsn suggestsMe: ABarray, beadarraySNP, BiocCaseStudies, BioNet, Category, categoryCompare, CMA, coGPS, dyebias, GeneSelector, GEOquery, GSRI, GSVA, Heatplus, inSilicoDb, les, lumi, methylumi, MLP, oligo, oneChannelGUI, PGSEA, plw, PREDA, puma, Rcade, RTopper, rtracklayer, virtualArray Package: limmaGUI Version: 1.34.0 Depends: limma, tcltk Suggests: statmod, R2HTML, xtable, tkrplot License: LGPL Title: GUI for limma package Description: A Graphical User Interface for the limma Microarray package biocViews: Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, Bioinformatics, DifferentialExpression, MultipleComparisons, GUI Author: James Wettenhall Division of Genetics and Bioinformatics, WEHI Maintainer: Keith Satterley URL: http://bioinf.wehi.edu.au/limmaGUI/ MD5sum: 5ab7710025eb35d8da4f2a5a364b3a94 source.ver: src/contrib/limmaGUI_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/limmaGUI_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/limmaGUI_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/limmaGUI_1.34.0.tgz vignettes: vignettes/limmaGUI/inst/doc/extract.pdf, vignettes/limmaGUI/inst/doc/limmaGUI.pdf, vignettes/limmaGUI/inst/doc/LinModIntro.pdf vignetteTitles: Extracting limma objects from limmaGUI files, limmaGUI Vignette, LinModIntro.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/limmaGUI/inst/doc/extract.R, vignettes/limmaGUI/inst/doc/limmaGUI.R htmlDocs: vignettes/limmaGUI/inst/doc/about.html, vignettes/limmaGUI/inst/doc/CustMenu.html, vignettes/limmaGUI/inst/doc/import.html, vignettes/limmaGUI/inst/doc/index.html, vignettes/limmaGUI/inst/doc/InputFiles.html, vignettes/limmaGUI/inst/doc/lgDevel.html, vignettes/limmaGUI/inst/doc/windowsFocus.html Package: LiquidAssociation Version: 1.12.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>=3) Title: LiquidAssociation Description: The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data. biocViews: Pathways, GeneExpression, CellBiology, Genetics, NetworkAnalysis, TimeCourse Author: Yen-Yi Ho Maintainer: Yen-Yi Ho MD5sum: 7bbac13304945a7ce494e87fb4bf5d84 source.ver: src/contrib/LiquidAssociation_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LiquidAssociation_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LiquidAssociation_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LiquidAssociation_1.12.0.tgz vignettes: vignettes/LiquidAssociation/inst/doc/LiquidAssociation.pdf vignetteTitles: LiquidAssociation Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LiquidAssociation/inst/doc/LiquidAssociation.R Package: lmdme Version: 1.0.0 Depends: R (>= 2.14.1), methods, limma, pls Imports: stats Suggests: stemHypoxia Enhances: parallel License: GPL (>=2) Title: Linear Model decomposition for Designed Multivariate Experiments Description: linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i) Flexible formula type interface, ii) Fast limma based implementation, iii) p and F values over deflacted coefficients and iv) ploting functions for PCA and PLS biocViews: Microarray, OneChannel, TwoChannel, Bioinformatics, Visualization, AssayDomains, DifferentialExpression, ExperimentData, Cancer Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://200.45.112.41/bdmg/?page_id=38 MD5sum: 3e366a217504abcff70850e1d1dd1f81 source.ver: src/contrib/lmdme_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/lmdme_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/lmdme_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lmdme_1.0.0.tgz vignettes: vignettes/lmdme/inst/doc/lmdme-vignette.pdf vignetteTitles: lmdme: linear model framework for PCA/PLS analysis of ANOVA decomposition on Designed Multivariate Experiments in R hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/lmdme/inst/doc/lmdme-vignette.R Package: LMGene Version: 2.14.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy Suggests: affydata License: LGPL Title: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays Description: LMGene package for analysis of microarray data using a linear model and glog data transformation biocViews: Microarray, Bioinformatics, DifferentialExpression, Preprocessing Author: David Rocke, Geun Cheol Lee, John Tillinghast, Blythe Durbin-Johnson, and Shiquan Wu Maintainer: Blythe Durbin-Johnson URL: http://dmrocke.ucdavis.edu/software.html MD5sum: 8d60bc5ae232d6dbc01f9ba5ab2941bb source.ver: src/contrib/LMGene_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LMGene_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LMGene_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LMGene_2.14.0.tgz vignettes: vignettes/LMGene/inst/doc/LMGene.pdf vignetteTitles: LMGene User's Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LMGene/inst/doc/LMGene.R Package: logicFS Version: 1.28.1 Depends: LogicReg, mcbiopi Suggests: genefilter, siggenes License: LGPL (>= 2) Title: Identification of SNP Interactions Description: Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification. biocViews: SNP, Classification, Genetics Author: Holger Schwender Maintainer: Holger Schwender MD5sum: 4f7818ffc0a1aefd8fb140fd5f97adee source.ver: src/contrib/logicFS_1.28.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/logicFS_1.28.1.zip win64.binary.ver: bin/windows64/contrib/2.15/logicFS_1.28.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/logicFS_1.28.1.tgz vignettes: vignettes/logicFS/inst/doc/logicFS.pdf vignetteTitles: logicFS Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/logicFS/inst/doc/logicFS.R Package: logitT Version: 1.16.0 Depends: affy Suggests: SpikeInSubset License: GPL (>= 2) Archs: i386, x64 Title: logit-t Package Description: The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R. biocViews: Microarray, DifferentialExpression Author: Tobias Guennel Maintainer: Tobias Guennel URL: http://www.bioconductor.org MD5sum: 63bd3f1eb9d61f4313ea5d56eda1e1df source.ver: src/contrib/logitT_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/logitT_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/logitT_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/logitT_1.16.0.tgz vignettes: vignettes/logitT/inst/doc/logitT.pdf vignetteTitles: logitT primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/logitT/inst/doc/logitT.R Package: lol Version: 1.6.0 Depends: penalized, Matrix Imports: Matrix, penalized, graphics, grDevices, stats License: GPL-2 Title: Lots Of Lasso Description: Various optimization methods for Lasso inference with matrix warpper Author: Yinyin Yuan Maintainer: Yinyin Yuan MD5sum: cd56d0955249060d0bc163022e34e5d5 source.ver: src/contrib/lol_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/lol_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/lol_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lol_1.6.0.tgz vignettes: vignettes/lol/inst/doc/lol.pdf vignetteTitles: An introduction to the lol package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/lol/inst/doc/lol.R Package: LPE Version: 1.32.0 Depends: R (>= 2.10) Imports: stats License: LGPL Title: Methods for analyzing microarray data using Local Pooled Error (LPE) method Description: This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library. biocViews: Microarray, Bioinformatics, DifferentialExpression Author: Nitin Jain , Michael O'Connell , Jae K. Lee . Includes R source code contributed by HyungJun Cho Maintainer: Nitin Jain URL: http://www.r-project.org, http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/, http://sourceforge.net/projects/r-lpe/ MD5sum: 6707dcb05f8cdb698ee9b09f3b2c1004 source.ver: src/contrib/LPE_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LPE_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LPE_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LPE_1.32.0.tgz vignettes: vignettes/LPE/inst/doc/LPE.pdf vignetteTitles: LPE test for microarray data with small number of replicates hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LPE/inst/doc/LPE.R dependsOnMe: LPEadj, PLPE importsMe: LPEadj suggestsMe: ABarray Package: LPEadj Version: 1.18.0 Depends: LPE Imports: LPE, stats License: LGPL Title: A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size. Description: Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment. biocViews: Microarray, Bioinformatics, Proteomics Author: Carl Murie , Robert Nadon Maintainer: Carl Murie MD5sum: c135ea6ab5f52865dc956a13a52884aa source.ver: src/contrib/LPEadj_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LPEadj_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LPEadj_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LPEadj_1.18.0.tgz vignettes: vignettes/LPEadj/inst/doc/LPEadj.pdf vignetteTitles: LPEadj test for microarray data with small number of replicates hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LPEadj/inst/doc/LPEadj.R Package: lumi Version: 2.10.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), nleqslv Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), annotate, Biobase (>= 2.5.5), lattice, mgcv (>= 1.4-0), hdrcde, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) Title: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays Description: The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays. biocViews: Microarray, OneChannel, Preprocessing, DNAMethylation, QualityControl, TwoChannel Author: Pan Du, Richard Bourgon, Gang Feng, Simon Lin Maintainer: Pan Du MD5sum: f1cd8a3c17c448efb5a5237062e100cd source.ver: src/contrib/lumi_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/lumi_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/lumi_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lumi_2.10.0.tgz vignettes: vignettes/lumi/inst/doc/Bioc2007_lumi_presentation.pdf, vignettes/lumi/inst/doc/IlluminaAnnotation.pdf, vignettes/lumi/inst/doc/lumi.pdf, vignettes/lumi/inst/doc/lumi_VST_evaluation.pdf, vignettes/lumi/inst/doc/methylationAnalysis.pdf vignetteTitles: Bioc2007_lumi_presentation.pdf, Resolve the inconsistency of Illumina identifiers through nuID, Using lumi A package processing Illumina Microarray, Evaluation of VST algorithm in lumi package, Analyze Illumina Infinium methylation microarray data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/lumi/inst/doc/IlluminaAnnotation.R, vignettes/lumi/inst/doc/lumi.R, vignettes/lumi/inst/doc/lumi_VST_evaluation.R, vignettes/lumi/inst/doc/methylationAnalysis.R dependsOnMe: arrayMvout importsMe: ffpe, methyAnalysis suggestsMe: beadarray, methylumi, tigre, virtualArray Package: LVSmiRNA Version: 1.8.0 Depends: R (>= 2.10), Biobase,quantreg,splines,MASS,limma,affy,methods, SparseM, vsn Imports: BiocGenerics, stats4 Enhances: multicore,snow, Rmpi License: GPL-2 Archs: i386, x64 Title: LVS normalization for Agilent miRNA data Description: Normalization of Agilent miRNA arrays. biocViews: Microarray,AgilentChip,OneChannel,Preprocessing Author: Stefano Calza, Suo Chen, Yudi Pawitam Maintainer: Stefano Calza MD5sum: 34800cb974d531b793d691d8e07b14dd source.ver: src/contrib/LVSmiRNA_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LVSmiRNA_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LVSmiRNA_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LVSmiRNA_1.8.0.tgz vignettes: vignettes/LVSmiRNA/inst/doc/LVSmiRNA.pdf vignetteTitles: LVSmiRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LVSmiRNA/inst/doc/LVSmiRNA.R Package: maanova Version: 1.28.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, stats, utils Suggests: qvalue, snow Enhances: Rmpi License: GPL (>= 2) Archs: i386, x64 Title: Tools for analyzing Micro Array experiments Description: Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree. biocViews: Microarray, DifferentialExpression, Clustering Author: Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui. Maintainer: Keith Sheppard URL: http://research.jax.org/faculty/churchill MD5sum: 111e616ea8d448adadadfc95309707bb source.ver: src/contrib/maanova_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maanova_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maanova_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maanova_1.28.0.tgz vignettes: vignettes/maanova/inst/doc/abf1fig.pdf, vignettes/maanova/inst/doc/hckidney.pdf, vignettes/maanova/inst/doc/maanova.pdf, vignettes/maanova/inst/doc/vgprofile.pdf vignetteTitles: abf1fig.pdf, hckidney.pdf, R/maanova HowTo, vgprofile.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/maanova/inst/doc/maanova.R Package: macat Version: 1.32.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem License: Artistic-2.0 Title: MicroArray Chromosome Analysis Tool Description: This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'. biocViews: Microarray, DifferentialExpression, Visualization Author: Benjamin Georgi, Matthias Heinig, Stefan Roepcke, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling MD5sum: 416903b83d43f0e83b17249e1a4d23ce source.ver: src/contrib/macat_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/macat_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/macat_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/macat_1.32.0.tgz vignettes: vignettes/macat/inst/doc/chrom6TkNN.pdf, vignettes/macat/inst/doc/chrom6T.pdf, vignettes/macat/inst/doc/evalkNN6.pdf, vignettes/macat/inst/doc/macat.pdf, vignettes/macat/inst/doc/Slidingchrom6s3.pdf vignetteTitles: chrom6TkNN.pdf, chrom6T.pdf, evalkNN6.pdf, MicroArray Chromosome Analysis Tool, Slidingchrom6s3.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/macat/inst/doc/macat.R Package: maCorrPlot Version: 1.28.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) Title: Visualize artificial correlation in microarray data Description: Graphically displays correlation in microarray data that is due to insufficient normalization biocViews: Microarray, Preprocessing, Visualization Author: Alexander Ploner Maintainer: Alexander Ploner URL: http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15799785 MD5sum: 6ae3166555f50731a85215bc4c0befac source.ver: src/contrib/maCorrPlot_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maCorrPlot_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maCorrPlot_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maCorrPlot_1.28.0.tgz vignettes: vignettes/maCorrPlot/inst/doc/maCorrPlot.pdf vignetteTitles: maCorrPlot Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/maCorrPlot/inst/doc/maCorrPlot.R Package: maDB Version: 1.30.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), affy (>= 1.23.4), pgUtils (>= 1.23.2), limma (>= 1.8.0), methods Suggests: annaffy (>= 1.6.2), biomaRt (>= 1.8.2), geneplotter License: LGPL (>= 2) Title: Microarray database and utility functions for microarray data analysis. Description: maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays. biocViews: Microarray,TwoChannel,OneChannel,Visualization Author: Johannes Rainer Maintainer: Johannes Rainer MD5sum: 2ab7ecb3c8f8489fce0aee755a1742bc source.ver: src/contrib/maDB_1.30.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maDB_1.30.0.tgz vignettes: vignettes/maDB/inst/doc/maDB-015.pdf, vignettes/maDB/inst/doc/maDB-016.pdf, vignettes/maDB/inst/doc/maDB.pdf vignetteTitles: maDB-015.pdf, maDB-016.pdf, maDB.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: made4 Version: 1.32.0 Depends: ade4, RColorBrewer,gplots,scatterplot3d Suggests: affy License: Artistic-2.0 Title: Multivariate analysis of microarray data using ADE4 Description: Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4. biocViews: Bioinformatics, Clustering, Classification, MultipleComparisons Author: Aedin Culhane Maintainer: Aedin Culhane URL: http://www.hsph.harvard.edu/researchers/aculhane.html MD5sum: 5d59b706329d45f41e7672fd0c205d5e source.ver: src/contrib/made4_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/made4_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/made4_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/made4_1.32.0.tgz vignettes: vignettes/made4/inst/doc/html3D.pdf, vignettes/made4/inst/doc/introduction.pdf vignetteTitles: html3D.pdf, introduction.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/made4/inst/doc/introduction.R dependsOnMe: bgafun Package: maigesPack Version: 1.22.0 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) Archs: i386, x64 Title: Functions to handle cDNA microarray data, including several methods of data analysis Description: This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data biocViews: Microarray, TwoChannel, Preprocessing, ConnectTools, DifferentialExpression, Clustering, Classification, GraphsAndNetworks Author: Gustavo H. Esteves , with contributions from Roberto Hirata Jr , E. Jordao Neves , Elier B. Cristo , Ana C. Simoes and Lucas Fahham Maintainer: Gustavo H. Esteves URL: http://www.maiges.org/en/software/ MD5sum: f1847469b9cd838a0e811113424fa180 source.ver: src/contrib/maigesPack_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maigesPack_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maigesPack_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maigesPack_1.22.0.tgz vignettes: vignettes/maigesPack/inst/doc/maigesPack_tutorial.pdf vignetteTitles: maigesPack Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/maigesPack/inst/doc/maigesPack_tutorial.R Package: makecdfenv Version: 1.36.0 Depends: R (>= 2.6.0), methods Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) Archs: i386, x64 Title: CDF Environment Maker Description: This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. biocViews: OneChannel, DataImport, Preprocessing Author: Rafael A. Irizarry , Laurent Gautier , Wolfgang Huber , Ben Bolstad Maintainer: James W. MacDonald MD5sum: c24082bfa9e64e8934b4e7c5fec60af3 source.ver: src/contrib/makecdfenv_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/makecdfenv_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/makecdfenv_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/makecdfenv_1.36.0.tgz vignettes: vignettes/makecdfenv/inst/doc/makecdfenv.pdf vignetteTitles: makecdfenv primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/makecdfenv/inst/doc/makecdfenv.R dependsOnMe: altcdfenvs Package: MANOR Version: 1.30.0 Depends: R (>= 2.10), GLAD Imports: GLAD, graphics, grDevices, stats, utils License: GPL-2 Archs: i386, x64 Title: CGH Micro-Array NORmalization Description: Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. biocViews: Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, CopyNumberVariants Author: Pierre Neuvial , Philippe Hupe Maintainer: Pierre Neuvial URL: http://bioinfo.curie.fr/projects/manor/index.html MD5sum: 4ae766ea1dffe4e7f09b180fd7f9d421 source.ver: src/contrib/MANOR_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MANOR_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MANOR_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MANOR_1.30.0.tgz vignettes: vignettes/MANOR/inst/doc/MANOR.pdf vignetteTitles: MANOR overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MANOR/inst/doc/MANOR.R htmlDocs: vignettes/MANOR/inst/doc/index.html Package: manta Version: 1.4.0 Depends: R (>= 1.8.0), methods, edgeR (>= 2.5.13) Imports: Hmisc, caroline(>= 0.6.6) Suggests: RSQLite, plotrix License: Artistic-2.0 Title: Microbial Assemblage Normalized Transcript Analysis Description: Tools for robust comparative metatranscriptomics. biocViews: DifferentialExpression, RNAseq, Genetics, GeneExpression, Bioinformatics, HighThroughputSequencing, QualityControl, DataImport, Visualization Author: David M. Schruth and Adrian Marchetti Maintainer: David M. Schruth URL: http://manta.ocean.washington.edu/ MD5sum: a025bb361ab997311fe1d6663c4acc10 source.ver: src/contrib/manta_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/manta_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/manta_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/manta_1.4.0.tgz vignettes: vignettes/manta/inst/doc/manta.pdf vignetteTitles: manta hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/manta/inst/doc/manta.R Package: MantelCorr Version: 1.28.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) Title: Compute Mantel Cluster Correlations Description: Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data). biocViews: Bioinformatics, Clustering Author: Brian Steinmeyer and William Shannon Maintainer: Brian Steinmeyer MD5sum: 8b92ae9f81d24ff399d8354bfd31d443 source.ver: src/contrib/MantelCorr_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MantelCorr_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MantelCorr_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MantelCorr_1.28.0.tgz vignettes: vignettes/MantelCorr/inst/doc/MantelCorrVignette.pdf vignetteTitles: MantelCorrVignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MantelCorr/inst/doc/MantelCorrVignette.R Package: marray Version: 1.36.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL Title: Exploratory analysis for two-color spotted microarray data Description: Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. biocViews: Microarray, TwoChannel, Preprocessing Author: Yee Hwa (Jean) Yang with contributions from Agnes Paquet and Sandrine Dudoit. Maintainer: Yee Hwa (Jean) Yang URL: http://www.maths.usyd.edu.au/u/jeany/ MD5sum: b1e405d59a2700942c441a67aa9b46cd source.ver: src/contrib/marray_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/marray_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/marray_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/marray_1.36.0.tgz vignettes: vignettes/marray/inst/doc/ExampleHTML.pdf, vignettes/marray/inst/doc/marrayClasses.pdf, vignettes/marray/inst/doc/marrayClassesShort.pdf, vignettes/marray/inst/doc/marrayInput.pdf, vignettes/marray/inst/doc/marrayNorm.pdf, vignettes/marray/inst/doc/marray.pdf, vignettes/marray/inst/doc/marrayPlots.pdf, vignettes/marray/inst/doc/widget1.pdf vignetteTitles: ExampleHTML.pdf, marrayClasses Overview, marrayClasses Tutorial (short), marrayInput Introduction, marray Normalization, marray Overview, marrayPlots Overview, widget1.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/marray/inst/doc/marrayClasses.R, vignettes/marray/inst/doc/marrayClassesShort.R, vignettes/marray/inst/doc/marrayInput.R, vignettes/marray/inst/doc/marrayNorm.R, vignettes/marray/inst/doc/marrayPlots.R, vignettes/marray/inst/doc/marray.R dependsOnMe: CGHbase, convert, dyebias, maigesPack, nnNorm, OLIN, stepNorm, TurboNorm importsMe: arrayQuality, nnNorm, OLIN, OLINgui, sigaR, stepNorm, timecourse suggestsMe: Agi4x44PreProcess, DEGraph, Mfuzz Package: maSigPro Version: 1.30.0 Depends: R (>= 2.3.1), stats, Biobase Imports: Biobase, graphics, grDevices, limma, Mfuzz, stats, utils License: GPL (>= 2) Title: Significant Gene Expression Profile Differences in Time Course Microarray Data Description: maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments. biocViews: Microarray, DifferentialExpression, TimeCourse Author: Ana Conesa , Maria Jose Nueda Maintainer: Maria Jose Nueda URL: http://bioinfo.cipf.es/ MD5sum: ec770eac34bb24fe38a581313d2dc6d4 source.ver: src/contrib/maSigPro_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maSigPro_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maSigPro_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maSigPro_1.30.0.tgz vignettes: vignettes/maSigPro/inst/doc/maSigPro-tutorial.pdf, vignettes/maSigPro/inst/doc/PLOTGROUPS.pdf, vignettes/maSigPro/inst/doc/PLOTPROFILES.pdf vignetteTitles: maSigPro User's Guide, PLOTGROUPS.pdf, PLOTPROFILES.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/maSigPro/inst/doc/maSigPro-tutorial.R suggestsMe: oneChannelGUI Package: maskBAD Version: 1.2.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe License: GPL version 2 or newer Title: Masking probes with binding affinity differences Description: Package includes functions to analyze and mask microarray expression data. Author: Michael Dannemann Maintainer: Michael Dannemann MD5sum: 891e46b431e2adabf72d3e1c31a7faa5 source.ver: src/contrib/maskBAD_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maskBAD_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maskBAD_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maskBAD_1.2.0.tgz vignettes: vignettes/maskBAD/inst/doc/maskBAD.pdf vignetteTitles: Package maskBAD hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/maskBAD/inst/doc/maskBAD.R Package: MassArray Version: 1.10.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, methods, stats, utils License: GPL (>=2) Title: Analytical Tools for MassArray Data Description: This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis. biocViews: DNAMethylation, SNP, MassSpectrometry, Genetics, DataImport, Visualization Author: Reid F. Thompson , John M. Greally Maintainer: Reid F. Thompson MD5sum: eb4b4bccba149dd1bb2706ee5a8a2e91 source.ver: src/contrib/MassArray_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MassArray_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MassArray_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MassArray_1.10.0.tgz vignettes: vignettes/MassArray/inst/doc/conversion.pdf, vignettes/MassArray/inst/doc/MassArray.pdf vignetteTitles: conversion.pdf, 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MassArray/inst/doc/MassArray.R Package: MassSpecWavelet Version: 1.24.0 Depends: waveslim Suggests: xcms, caTools License: LGPL (>= 2) Archs: i386, x64 Title: Mass spectrum processing by wavelet-based algorithms Description: Processing Mass Spectrometry spectrum by using wavelet based algorithm biocViews: MassSpectrometry, Proteomics Author: Pan Du, Warren Kibbe, Simon Lin Maintainer: Pan Du MD5sum: 25aabf5a70717b880d0af44feffb352a source.ver: src/contrib/MassSpecWavelet_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MassSpecWavelet_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MassSpecWavelet_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MassSpecWavelet_1.24.0.tgz vignettes: vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.pdf vignetteTitles: MassSpecWavelet hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.R suggestsMe: xcms Package: matchBox Version: 1.0.0 Depends: R (>= 2.8.0) License: Artistic-2.0 Title: Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis. Description: The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance. biocViews: Software, Annotation, Microarray, MultipleComparisons, Visualization Author: Luigi Marchionni , Anuj Gupta Maintainer: Luigi Marchionni , Anuj Gupta MD5sum: a159d3526485e6082817d1d7052b516a source.ver: src/contrib/matchBox_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/matchBox_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/matchBox_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/matchBox_1.0.0.tgz vignettes: vignettes/matchBox/inst/doc/matchBox.pdf vignetteTitles: Working with the matchBox package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/matchBox/inst/doc/matchBox.R Package: MBCB Version: 1.12.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) Title: MBCB (Model-based Background Correction for Beadarray) Description: This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data. biocViews: Microarray, Preprocessing Author: Yang Xie Maintainer: Jeff Allen URL: http://www.utsouthwestern.edu MD5sum: b3afc59686153498bee60e52961cff72 source.ver: src/contrib/MBCB_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MBCB_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MBCB_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MBCB_1.12.0.tgz vignettes: vignettes/MBCB/inst/doc/MBCB.pdf vignetteTitles: MBCB hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MBCB/inst/doc/MBCB.R Package: mBPCR Version: 1.12.0 Depends: oligoClasses, SNPchip Imports: Biobase Suggests: xtable License: GPL (>= 2) Title: Bayesian Piecewise Constant Regression for DNA copy number estimation Description: Estimates the DNA copy number profile using mBPCR to detect regions with copy number changes biocViews: aCGH, SNP, Microarray, CopyNumberVariants, Bioinformatics Author: P.M.V. Rancoita , with contributions from M. Hutter Maintainer: P.M.V. Rancoita URL: http://www.idsia.ch/~paola/mBPCR MD5sum: 9e301d6a30c44f6a6892483580857c2c source.ver: src/contrib/mBPCR_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mBPCR_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mBPCR_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mBPCR_1.12.0.tgz vignettes: vignettes/mBPCR/inst/doc/mBPCR.pdf vignetteTitles: mBPCR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mBPCR/inst/doc/mBPCR.R Package: mcaGUI Version: 1.6.0 Depends: lattice, MASS, proto, foreign, gWidgets(>= 0.0-36), gWidgetsRGtk2(>= 0.0-53), OTUbase, vegan, bpca Enhances: iplots, reshape, ggplot2, cairoDevice, OTUbase License: GPL (>= 2) Title: Microbial Community Analysis GUI Description: Microbial community analysis GUI for R using gWidgets. biocViews: GUI, Visualization, Bioinformatics, Clustering, Sequencing Author: Wade K. Copeland, Vandhana Krishnan, Daniel Beck, Matt Settles, James Foster, Kyu-Chul Cho, Mitch Day, Roxana Hickey, Ursel M.E. Schutte, Xia Zhou, Chris Williams, Larry J. Forney, Zaid Abdo, Poor Man's GUI (PMG) base code by John Verzani with contributions by Yvonnick Noel Maintainer: Wade K. Copeland URL: http://www.ibest.uidaho.edu/ibest/index.php MD5sum: 3072aff15847feb23bddbb5aa949ce58 source.ver: src/contrib/mcaGUI_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mcaGUI_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mcaGUI_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mcaGUI_1.6.0.tgz vignettes: vignettes/mcaGUI/inst/doc/An_Introduction_and_User_Guide_for_mcaGUI.pdf vignetteTitles: An_Introduction_and_User_Guide_for_mcaGUI.pdf hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MCRestimate Version: 2.14.0 Depends: R (>= 2.7.2), golubEsets (>= 1.4.6) Imports: e1071 (>= 1.5-12), pamr (>= 1.22), randomForest (>= 3.9-6), RColorBrewer (>= 0.1-3), Biobase (>= 2.5.5), graphics, grDevices, stats, utils Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0), gpls (>= 1.6.0) License: GPL (>= 2) Title: Misclassification error estimation with cross-validation Description: This package includes a function for combining preprocessing and classification methods to calculate misclassification errors biocViews: Bioinformatics, Classification Author: Marc Johannes, Markus Ruschhaupt, Holger Froehlich, Ulrich Mansmann, Andreas Buness, Patrick Warnat, Wolfgang Huber, Axel Benner, Tim Beissbarth Maintainer: Marc Johannes MD5sum: 92772cd9ad8d0b6a7ce24ab655de0417 source.ver: src/contrib/MCRestimate_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MCRestimate_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MCRestimate_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MCRestimate_2.14.0.tgz vignettes: vignettes/MCRestimate/inst/doc/UsingMCRestimate.pdf vignetteTitles: HOW TO use MCRestimate hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MCRestimate/inst/doc/UsingMCRestimate.R Package: mdqc Version: 1.20.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) Title: Mahalanobis Distance Quality Control for microarrays Description: MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. biocViews: Microarray, QualityControl Author: Justin Harrington Maintainer: Gabriela Cohen-Freue MD5sum: 2dfde48bee9eeefcc3866057bc6e6f12 source.ver: src/contrib/mdqc_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mdqc_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mdqc_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mdqc_1.20.0.tgz vignettes: vignettes/mdqc/inst/doc/mdqcvignette.pdf vignetteTitles: Introduction to MDQC hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mdqc/inst/doc/mdqcvignette.R importsMe: arrayMvout Package: MeasurementError.cor Version: 1.30.0 License: LGPL Title: Measurement Error model estimate for correlation coefficient Description: Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation biocViews: Bioinformatics Author: Beiying Ding Maintainer: Beiying Ding MD5sum: ff4cbd68dc0c7b3a754b927c3c6bb643 source.ver: src/contrib/MeasurementError.cor_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MeasurementError.cor_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MeasurementError.cor_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MeasurementError.cor_1.30.0.tgz vignettes: vignettes/MeasurementError.cor/inst/doc/MeasurementError.cor.pdf vignetteTitles: MeasurementError.cor Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEDIPS Version: 1.8.0 Depends: R (>= 2.12.0), BiocGenerics (>= 0.1.3), BSgenome Imports: methods, BiocGenerics, Biostrings, BSgenome, graphics, gtools, IRanges, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19 License: GPL (>=2) Archs: i386, x64 Title: MeDIP-Seq data analysis Description: MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-Seq). Nevertheless, functionalities like the quality controls may be applied to other types of sequencing data (e.g. ChIP-Seq). MEDIPS adresses several aspects in the context of MeDIP-Seq data analysis. biocViews: Sequencing, DNAMethylation, CpGIsland, DifferentialExpression, HighThroughputSequencing, ChIPseq, Preprocessing, QualityControl, Visualization, Methylseq Author: Lukas Chavez, Joern Dietrich Maintainer: Lukas Chavez MD5sum: ac88cdeb476f76506c9aebbb30812288 source.ver: src/contrib/MEDIPS_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MEDIPS_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MEDIPS_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MEDIPS_1.8.0.tgz vignettes: vignettes/MEDIPS/inst/doc/MEDIPS.pdf vignetteTitles: MEDIPS hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MEDIPS/inst/doc/MEDIPS.R Package: MEDME Version: 1.18.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) Archs: i386, x64 Title: Modelling Experimental Data from MeDIP Enrichment Description: Description: MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments biocViews: Microarray, CpGIsland, DNAMethylation Author: Mattia Pelizzola and Annette Molinaro Maintainer: Mattia Pelizzola MD5sum: 53f7ded7a0dba349f408b5bd7d50d38c source.ver: src/contrib/MEDME_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MEDME_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MEDME_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MEDME_1.18.0.tgz vignettes: vignettes/MEDME/inst/doc/MEDME.pdf vignetteTitles: MEDME.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MEDME/inst/doc/MEDME.R Package: MergeMaid Version: 2.30.0 Depends: R (>= 2.10.0), survival, Biobase, MASS, methods License: GPL (>= 2) Title: Merge Maid Description: The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival. biocViews: Microarray, DifferentialExpression, Visualization Author: Xiaogang Zhong Leslie Cope Elizabeth Garrett Giovanni Parmigiani Maintainer: Xiaogang Zhong URL: http://astor.som.jhmi.edu/MergeMaid MD5sum: dec227a3688fac6fe484d2722e401c9f source.ver: src/contrib/MergeMaid_2.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MergeMaid_2.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MergeMaid_2.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MergeMaid_2.30.0.tgz vignettes: vignettes/MergeMaid/inst/doc/MergeMaid.pdf vignetteTitles: MergeMaid primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MergeMaid/inst/doc/MergeMaid.R importsMe: metaArray, XDE suggestsMe: oneChannelGUI Package: metaArray Version: 1.36.0 Imports: Biobase, MergeMaid, graphics, stats License: LGPL-2 Archs: i386, x64 Title: Integration of Microarray Data for Meta-analysis Description: 1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform biocViews: Microarray, Bioinformatics, DifferentialExpression Author: Debashis Ghosh Hyungwon Choi Maintainer: Hyungwon Choi MD5sum: 90680bc0b3a860e8acc4dd3824db3148 source.ver: src/contrib/metaArray_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/metaArray_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/metaArray_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/metaArray_1.36.0.tgz vignettes: vignettes/metaArray/inst/doc/metaArray.pdf vignetteTitles: metaArray Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/metaArray/inst/doc/metaArray.R suggestsMe: oneChannelGUI Package: metahdep Version: 1.16.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 Archs: i386, x64 Title: Hierarchical Dependence in Meta-Analysis Description: Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies biocViews: Microarray, Bioinformatics, DifferentialExpression Author: John R. Stevens, Gabriel Nicholas Maintainer: John R. Stevens MD5sum: 4635f23d52793a5834b555e02938b880 source.ver: src/contrib/metahdep_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/metahdep_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/metahdep_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/metahdep_1.16.0.tgz vignettes: vignettes/metahdep/inst/doc/metahdep.pdf vignetteTitles: metahdep Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/metahdep/inst/doc/metahdep.R Package: methVisual Version: 1.10.0 Depends: R (>= 2.11.0), Biostrings(>= 2.4.8), plotrix,gsubfn, grid,sqldf Imports: Biostrings, ca, graphics, grDevices, grid, gridBase, IRanges, stats, utils License: GPL (>= 2) Title: Methods for visualization and statistics on DNA methylation data Description: The package 'methVisual' allows the visualization of DNA methylation data after bisulfite sequencing. biocViews: Bioinformatics, DNAMethylation, Clustering, Classification Author: A. Zackay, C. Steinhoff Maintainer: Arie Zackay MD5sum: 77e46515182dbb940622c943c3154183 source.ver: src/contrib/methVisual_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/methVisual_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/methVisual_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/methVisual_1.10.0.tgz vignettes: vignettes/methVisual/inst/doc/methVisual.pdf vignetteTitles: Introduction to methVisual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/methVisual/inst/doc/methVisual.R Package: methyAnalysis Version: 1.0.0 Depends: R (>= 2.10), grid, IRanges, Biobase (>= 2.5.5), org.Hs.eg.db Imports: lumi, methylumi, Gviz, genoset, GenomicRanges, IRanges, rtracklayer, GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods Suggests: IlluminaHumanMethylation450k.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Title: DNA methylation data analysis and visualization Description: The methyAnalysis package aims for the DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focus on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data. biocViews: Microarray, DNAMethylation, Visualization Author: Pan Du, Richard Bourgon Maintainer: Pan Du MD5sum: 24a2e2bdb3b1153d96521a35744d9f62 source.ver: src/contrib/methyAnalysis_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/methyAnalysis_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/methyAnalysis_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/methyAnalysis_1.0.0.tgz vignettes: vignettes/methyAnalysis/inst/doc/methyAnalysis.pdf vignetteTitles: An Introduction to the methyAnalysis package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/methyAnalysis/inst/doc/methyAnalysis.R Package: methylumi Version: 2.4.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2 Imports: Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, stats4, BiocGenerics Suggests: lumi, lattice, limma, xtable, IlluminaHumanMethylation27k.db (>= 1.4.4), IlluminaHumanMethylation450k.db, SQN, MASS, matrixStats, parallel License: GPL-2 Title: Handle Illumina methylation data Description: This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included. biocViews: DNAMethylation, TwoChannel, Preprocessing, QualityControl, CpGIsland Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla Maintainer: Sean Davis MD5sum: 7360576a19ced4f94995b4a787694a53 source.ver: src/contrib/methylumi_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/methylumi_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/methylumi_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/methylumi_2.4.0.tgz vignettes: vignettes/methylumi/inst/doc/methylumi.pdf vignetteTitles: An Introduction to the methylumi package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/methylumi/inst/doc/methylumi.R importsMe: ffpe, lumi, methyAnalysis Package: Mfuzz Version: 2.16.1 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 Title: Soft clustering of time series gene expression data Description: Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface) biocViews: Microarray, Clustering, TimeCourse, Preprocessing, Visualization Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ MD5sum: fae6f79b0d1fc85fb9dcdf1b5648776b source.ver: src/contrib/Mfuzz_2.16.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/Mfuzz_2.16.1.zip win64.binary.ver: bin/windows64/contrib/2.15/Mfuzz_2.16.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Mfuzz_2.16.1.tgz vignettes: vignettes/Mfuzz/inst/doc/MfuzzguiScreenshot.pdf, vignettes/Mfuzz/inst/doc/Mfuzz.pdf, vignettes/Mfuzz/inst/doc/yeasttable3.pdf vignetteTitles: MfuzzguiScreenshot.pdf, Introduction to Mfuzz, yeasttable3.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Mfuzz/inst/doc/Mfuzz.R dependsOnMe: cycle importsMe: maSigPro Package: mgsa Version: 1.6.0 Depends: R (>= 2.9.0), methods, gplots Imports: gplots, graphics, stats, utils Suggests: DBI, RSQLite, GO.db License: Artistic-2.0 Archs: i386, x64 Title: Model-based gene set analysis Description: Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology. biocViews: Pathways, GO, GeneSetEnrichment Author: Sebastian Bauer , Julien Gagneur Maintainer: Sebastian Bauer MD5sum: 487822e9ec8ea974ed41d3a8ba63d17d source.ver: src/contrib/mgsa_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mgsa_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mgsa_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mgsa_1.6.0.tgz vignettes: vignettes/mgsa/inst/doc/mgsa.pdf vignetteTitles: Overview of the mgsa package. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mgsa/inst/doc/mgsa.R Package: MiChip Version: 1.12.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) Title: MiChip Parsing and Summarizing Functions Description: This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages. biocViews: Microarray, Preprocessing Author: Jonathon Blake Maintainer: Jonathon Blake MD5sum: 4db67b3207869418b213cc4abce27ead source.ver: src/contrib/MiChip_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MiChip_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MiChip_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MiChip_1.12.0.tgz vignettes: vignettes/MiChip/inst/doc/MiChip.pdf vignetteTitles: MiChip miRNA Microarray Processing hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MiChip/inst/doc/MiChip.R Package: microRNA Version: 1.16.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) Suggests: Biostrings (>= 2.11.32) Enhances: Rlibstree License: Artistic-2.0 Title: Data and functions for dealing with microRNAs Description: Different data resources for microRNAs and some functions for manipulating them. biocViews: Infrastructure, SequenceAnnotation, SequenceMatching Author: R. Gentleman, S. Falcon Maintainer: "James F. Reid" MD5sum: bc4280b3d0fc9acc14f9e3e9664d375e source.ver: src/contrib/microRNA_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/microRNA_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/microRNA_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/microRNA_1.16.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MmPalateMiRNA, rtracklayer Package: minet Version: 3.12.0 Depends: infotheo License: file LICENSE Archs: i386, x64 Title: Mutual Information NETworks Description: This package implements various algorithms for inferring mutual information networks from data. biocViews: Microarray, GraphsAndNetworks, NetworkAnalysis, NetworkInference Author: Patrick E. Meyer, Frederic Lafitte, Gianluca Bontempi Maintainer: Patrick E. Meyer URL: http://minet.meyerp.com MD5sum: 65b5df351fe5cf71ed1b5582132c4c28 source.ver: src/contrib/minet_3.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/minet_3.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/minet_3.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/minet_3.12.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: BUS, netresponse suggestsMe: predictionet Package: minfi Version: 1.4.0 Depends: methods, BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), lattice, reshape, GenomicRanges, Biostrings, utils Imports: BiocGenerics, beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, crlmm, matrixStats, mclust Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), minfiData (>= 0.2.0), RUnit License: Artistic-2.0 Title: Analyze Illumina's 450k methylation arrays Description: Tools for analyzing and visualizing Illumina's 450k array data biocViews: DNAMethylation, Microarray, TwoChannel, DataImport, Preprocessing, QualityControl Author: Kasper Daniel Hansen, Martin Aryee Maintainer: Kasper Daniel Hansen MD5sum: 2155ef1da26c026e7b34fc24679b9085 source.ver: src/contrib/minfi_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/minfi_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/minfi_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/minfi_1.4.0.tgz vignettes: vignettes/minfi/inst/doc/minfi.pdf vignetteTitles: Minfi Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/minfi/inst/doc/minfi.R Package: MinimumDistance Version: 1.2.4 Depends: R (>= 2.14), BiocGenerics (>= 0.3.2), IRanges (>= 1.13.30) Imports: methods, DNAcopy, utils, msm, lattice, BiocGenerics, VanillaICE (>= 1.19.23), ff, SNPchip (>= 2.3.10), Biobase (>= 2.17.8), foreach, oligoClasses (>= 1.19.34), GenomicRanges Suggests: human610quadv1bCrlmm, RUnit Enhances: snow, doSNOW License: Artistic-2.0 Title: A package for de novo CNV detection in case-parent trios Description: Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms biocViews: Microarray, SNP, Bioinformatics, CopyNumberVariants Author: Robert B Scharpf, Moiz Bootwalla, and Ingo Ruczinski Maintainer: Robert B Scharpf MD5sum: 16802f4297ad3d00938b11e7a8340b24 source.ver: src/contrib/MinimumDistance_1.2.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/MinimumDistance_1.2.4.zip win64.binary.ver: bin/windows64/contrib/2.15/MinimumDistance_1.2.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MinimumDistance_1.2.4.tgz vignettes: vignettes/MinimumDistance/inst/doc/MinimumDistance.pdf vignetteTitles: Detection of de novo copy number alterations in case-parent trios hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MinimumDistance/inst/doc/MinimumDistance.R Package: MiPP Version: 1.30.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) Title: Misclassification Penalized Posterior Classification Description: This package finds optimal sets of genes that seperate samples into two or more classes. biocViews: Microarray, Classification Author: HyungJun Cho , Sukwoo Kim , Mat Soukup , and Jae K. Lee Maintainer: Sukwoo Kim URL: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ MD5sum: 73d94a55c1f34d616235772b80ac78f9 source.ver: src/contrib/MiPP_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MiPP_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MiPP_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MiPP_1.30.0.tgz vignettes: vignettes/MiPP/inst/doc/MiPP.pdf vignetteTitles: MiPP Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MiPP/inst/doc/MiPP.R Package: MiRaGE Version: 1.0.0 Depends: R (>= 2.12.1), Biobase(>= 2.16.0) Imports: AnnotationDbi, BiocGenerics Suggests: seqinr (>= 3.0.3), biomaRt (>= 2.6.0), GenomicFeatures (>= 1.8.1), Biostrings (>= 2.24.1), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, miRNATarget, humanStemCell, IRanges , GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL Title: MiRNA Ranking by Gene Expression Description: The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile. biocViews: Microarray, GeneExpression, RNAseq, RNAseqData, HighThroughputSequencingData, Sequencing, SAGE Author: Y-h. Taguchi Maintainer: Y-h. Taguchi MD5sum: 48b4acb3c24585fc85957b34ac38eda7 source.ver: src/contrib/MiRaGE_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MiRaGE_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MiRaGE_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MiRaGE_1.0.0.tgz vignettes: vignettes/MiRaGE/inst/doc/MiRaGE.pdf vignetteTitles: How to use MiRaGE Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MiRaGE/inst/doc/MiRaGE.R Package: miRNApath Version: 1.18.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 Title: miRNApath: Pathway Enrichment for miRNA Expression Data Description: This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes. biocViews: Annotation, Pathways, DifferentialExpression, NetworkEnrichment, miRNA Author: James M. Ward with contributions from Yunling Shi, Cindy Richards, John P. Cogswell Maintainer: James M. Ward MD5sum: 1ef3291851b9d45cf2b1c440495c0944 source.ver: src/contrib/miRNApath_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/miRNApath_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/miRNApath_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/miRNApath_1.18.0.tgz vignettes: vignettes/miRNApath/inst/doc/miRNApath.pdf vignetteTitles: miRNApath: Pathway Enrichment for miRNA Expression Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/miRNApath/inst/doc/miRNApath.R Package: MLInterfaces Version: 1.38.1 Depends: R (>= 2.9), Biobase, MASS, methods, genefilter, rpart, rda, annotate, cluster, sfsmisc Imports: mboost, gdata, pls Suggests: class, e1071, ipred, randomForest, gpls, pamr, rpart, MASS, nnet, ALL, gbm, mlbench, hgu95av2.db, som, RColorBrewer, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, gbm, mboost, sfsmisc, party Enhances: parallel License: LGPL Title: Uniform interfaces to R machine learning procedures for data in Bioconductor containers Description: Uniform interfaces to machine learning code for data in Bioconductor containers biocViews: Bioinformatics, Classification, Clustering Author: Vince Carey , Robert Gentleman, Jess Mar, and contributions from Jason Vertrees and Laurent Gatto Maintainer: V. Carey MD5sum: 0fa16ef7e6bd7009b26031a268b283a0 source.ver: src/contrib/MLInterfaces_1.38.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/MLInterfaces_1.38.1.zip win64.binary.ver: bin/windows64/contrib/2.15/MLInterfaces_1.38.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MLInterfaces_1.38.1.tgz vignettes: vignettes/MLInterfaces/inst/doc/MLint_devel.pdf, vignettes/MLInterfaces/inst/doc/MLInterfaces.pdf, vignettes/MLInterfaces/inst/doc/MLprac2_2.pdf, vignettes/MLInterfaces/inst/doc/xvalComputerClusters.pdf vignetteTitles: MLInterfaces devel for schema-based MLearn, MLInterfaces Primer, A machine learning tutorial: applications of the Bioconductor MLInterfaces package to expression and ChIP-Seq data, MLInterfaces Computer Cluster hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MLInterfaces/inst/doc/MLint_devel.R, vignettes/MLInterfaces/inst/doc/MLInterfaces.R, vignettes/MLInterfaces/inst/doc/MLprac2_2.R, vignettes/MLInterfaces/inst/doc/xvalComputerClusters.R dependsOnMe: a4Classif suggestsMe: BiocCaseStudies Package: MLP Version: 1.6.0 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 Title: MLP Description: Mean Log P Analysis biocViews: Genetics Author: Nandini Raghavan, Tobias Verbeke, An De Bondt with contributions by Javier Cabrera, Dhammika Amaratunga, Tine Casneuf and Willem Ligtenberg Maintainer: Tobias Verbeke MD5sum: b3ebe9abcbff9b0cae6c88cb85dded03 source.ver: src/contrib/MLP_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MLP_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MLP_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MLP_1.6.0.tgz vignettes: vignettes/MLP/inst/doc/UsingMLP.pdf vignetteTitles: UsingMLP hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MLP/inst/doc/UsingMLP.R suggestsMe: a4 Package: MmPalateMiRNA Version: 1.6.0 Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod, lattice, vsn Imports: limma, lattice, Biobase Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra License: LGPL-3 Title: Murine Palate miRNA Expression Analysis Description: R package compendium for the analysis of murine palate miRNA two-color expression data. biocViews: Microarray, TwoChannel, Bioinformatics, QualityControl, Preprocessing, DifferentialExpression, MultipleComparisons, Clustering, GO, Pathways, ReportWriting, SequenceMatching Author: Guy Brock , Partha Mukhopadhyay , Vasyl Pihur , Robert M. Greene , and M. Michele Pisano Maintainer: Guy Brock MD5sum: d2a6eb3d4c877c86605debe186b9ebe5 source.ver: src/contrib/MmPalateMiRNA_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MmPalateMiRNA_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MmPalateMiRNA_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MmPalateMiRNA_1.6.0.tgz vignettes: vignettes/MmPalateMiRNA/inst/doc/MmPalateMiRNA.pdf vignetteTitles: Palate miRNA Analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MmPalateMiRNA/inst/doc/MmPalateMiRNA.R Package: mosaics Version: 1.6.0 Depends: R (>= 2.11.1), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) Archs: i386, x64 Title: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) Description: This package provides functions for fitting MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data. biocViews: ChIPseq, Sequencing, Transcription, Genetics, Bioinformatics Author: Dongjun Chung, Pei Fen Kuan, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group SystemRequirements: Perl MD5sum: d3ecbfe9ab430254a1ebe3c15a63e2d7 source.ver: src/contrib/mosaics_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mosaics_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mosaics_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mosaics_1.6.0.tgz vignettes: vignettes/mosaics/inst/doc/Figure4a.pdf, vignettes/mosaics/inst/doc/Figure4b.pdf, vignettes/mosaics/inst/doc/Figure5a.pdf, vignettes/mosaics/inst/doc/Figure5b.pdf, vignettes/mosaics/inst/doc/Figure5c.pdf, vignettes/mosaics/inst/doc/Figure5d.pdf, vignettes/mosaics/inst/doc/GOF_matchLow.pdf, vignettes/mosaics/inst/doc/GOF_rMOM.pdf, vignettes/mosaics/inst/doc/mosaics-example.pdf vignetteTitles: Figure4a.pdf, Figure4b.pdf, Figure5a.pdf, Figure5b.pdf, Figure5c.pdf, Figure5d.pdf, GOF_matchLow.pdf, GOF_rMOM.pdf, MOSAiCS hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mosaics/inst/doc/mosaics-example.R Package: MotifDb Version: 1.0.0 Depends: R (>= 2.15.0), methods, IRanges, Biostrings Imports: BiocGenerics, rtracklayer Suggests: RUnit, MotIV, seqLogo License: Artistic-2.0 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs Description: More than 2000 annotated position frequency matrices from five public source, for multiple organisms biocViews: GenomicSequence, MotifAnnotation Author: Paul Shannon Maintainer: Paul Shannon MD5sum: 6c23b6bfac7a679134b7ff4371ac36dc source.ver: src/contrib/MotifDb_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MotifDb_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MotifDb_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MotifDb_1.0.0.tgz vignettes: vignettes/MotifDb/inst/doc/MotifDb.pdf vignetteTitles: MotifDb Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MotifDb/inst/doc/MotifDb.R Package: motifRG Version: 1.2.0 Depends: R (>= 2.10) Imports: Biostrings, IRanges, seqLogo, parallel, methods, grid,graphics License: Artistic-2.0 Title: A package for discriminative motif discovery, designed for high throughput sequencing dataset Description: Tools for discriminative motif discovery using regression methods biocViews: Transcription, MotifDiscovery Author: Zizhen Yao Maintainer: Zizhen Yao MD5sum: 99d4aaad97edb2d3d45e70e0161a9bd3 source.ver: src/contrib/motifRG_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/motifRG_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/motifRG_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/motifRG_1.2.0.tgz vignettes: vignettes/motifRG/inst/doc/motifRG.pdf vignetteTitles: motifRG: regression-based discriminative motif discovery hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/motifRG/inst/doc/motifRG.R Package: motifStack Version: 1.0.4 Depends: R (>= 2.15.1), methods, grImport Imports: grImport, grid, XML Suggests: RUnit, BiocGenerics, MotIV License: GPL (>= 2) Title: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence Description: The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors. biocViews: SequenceMatching, GenomicsSequence, Visualization Author: Jianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu Maintainer: Jianhong Ou MD5sum: 8933648d829df9b43097a430acac2377 source.ver: src/contrib/motifStack_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/motifStack_1.0.4.zip win64.binary.ver: bin/windows64/contrib/2.15/motifStack_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/motifStack_1.0.4.tgz vignettes: vignettes/motifStack/inst/doc/motifStack.pdf vignetteTitles: motifStack Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/motifStack/inst/doc/motifStack.R Package: MotIV Version: 1.14.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.0) Imports: graphics, grid, methods, BiocGenerics, IRanges (>= 1.13.5), Biostrings (>= 1.24.0), lattice, rGADEM, stats, utils Suggests: rtracklayer License: GPL-2 Archs: i386, x64 Title: Motif Identification and Validation Description: This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs. biocViews: Microarray, ChIPchip, ChIPseq, GenomicSequence, MotifAnnotation Author: Eloi Mercier, Raphael Gottardo Maintainer: Eloi Mercier , Raphael Gottardo MD5sum: 454b28721a332a5a98192c11a6d8b9c5 source.ver: src/contrib/MotIV_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MotIV_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MotIV_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MotIV_1.14.0.tgz vignettes: vignettes/MotIV/inst/doc/MotIV.pdf vignetteTitles: The MotIV users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MotIV/inst/doc/MotIV.R suggestsMe: MotifDb, motifStack Package: MSnbase Version: 1.6.2 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.3), Biobase (>= 2.15.2), ggplot2, mzR Imports: plyr, IRanges, preprocessCore, vsn, grid, reshape2, stats4, affy Suggests: testthat, zoo, knitr, rols, Rdisop Enhances: foreach, doMC, parallel License: Artistic-2.0 Title: MSnbase: Base Functions and Classes for MS-based Proteomics Description: Basic plotting, data manipulation and processing of MS-based Proteomics data biocViews: Infrastructure, Bioinformatics, Proteomics, MassSpectrometry Author: Laurent Gatto with contributions from Guangchuang Yu Maintainer: Laurent Gatto MD5sum: e0a6599f48af7ce2d40446d3c2c9c1cf source.ver: src/contrib/MSnbase_1.6.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/MSnbase_1.6.2.zip win64.binary.ver: bin/windows64/contrib/2.15/MSnbase_1.6.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MSnbase_1.6.2.tgz vignettes: vignettes/MSnbase/inst/doc/itraqchem.pdf, vignettes/MSnbase/inst/doc/MSnbase-demo.pdf, vignettes/MSnbase/inst/doc/MSnbase-development.pdf, vignettes/MSnbase/inst/doc/MSnbase-io.pdf, vignettes/MSnbase/inst/doc/plotMzDelta-pride12011.pdf vignetteTitles: itraqchem.pdf, Base Functions and Classes for MS-based Proteomics, MSnbase development, MSnbase IO capabilities, plotMzDelta-pride12011.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSnbase/inst/doc/MSnbase-demo.R, vignettes/MSnbase/inst/doc/MSnbase-development.R, vignettes/MSnbase/inst/doc/MSnbase-io.R dependsOnMe: synapter suggestsMe: isobar Package: Mulcom Version: 1.8.0 Depends: R (>= 2.10), fields, Biobase Imports: graphics, grDevices, stats, methods License: GPL-2 Archs: i386, x64 Title: Calculates Mulcom test Description: Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test biocViews: Statistics, MultipleComparisons, Microarray, DifferentialExpression, GeneExpression Author: Claudio Isella Maintainer: Claudio Isella MD5sum: 8be6b3edc8c72bf715866d309432e7aa source.ver: src/contrib/Mulcom_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Mulcom_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Mulcom_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Mulcom_1.8.0.tgz vignettes: vignettes/Mulcom/inst/doc/MulcomVignette.pdf vignetteTitles: Mulcom Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Mulcom/inst/doc/MulcomVignette.R Package: multiscan Version: 1.18.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) Archs: i386, x64 Title: R package for combining multiple scans Description: Estimates gene expressions from several laser scans of the same microarray biocViews: Microarray, Preprocessing Author: Mizanur Khondoker , Chris Glasbey, Bruce Worton. Maintainer: Mizanur Khondoker MD5sum: 5e1d96439e475de18d2a65d464f6bdca source.ver: src/contrib/multiscan_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/multiscan_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/multiscan_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/multiscan_1.18.0.tgz vignettes: vignettes/multiscan/inst/doc/multiscan.pdf vignetteTitles: An R Package for Estimating Gene Expressions using Multiple Scans hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/multiscan/inst/doc/multiscan.R Package: multtest Version: 2.14.0 Depends: R (>= 2.10), methods, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL Archs: i386, x64 Title: Resampling-based multiple hypothesis testing Description: Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. biocViews: Microarray, DifferentialExpression, MultipleComparisons Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit Maintainer: Katherine S. Pollard MD5sum: 2cbfe12636fc0865e8fc3fe56272fa5f source.ver: src/contrib/multtest_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/multtest_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/multtest_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/multtest_2.14.0.tgz vignettes: vignettes/multtest/inst/doc/MTPALL.pdf, vignettes/multtest/inst/doc/MTP.pdf, vignettes/multtest/inst/doc/multtest.pdf vignetteTitles: MTPALL.pdf, MTP.pdf, multtest.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4Base, aCGH, BicARE, ChIPpeakAnno, gage, iPAC, KCsmart, LMGene, PREDA, REDseq, SAGx, siggenes, webbioc importsMe: ABarray, aCGH, adSplit, anota, ChIPpeakAnno, GeneSelector, globaltest, IsoGeneGUI, OCplus, phyloseq, REDseq, RTopper, synapter, webbioc suggestsMe: annaffy, BiocCaseStudies, ecolitk, factDesign, GeneSelector, GOstats, GSEAlm, maigesPack, MmPalateMiRNA, oneChannelGUI, pcot2, safe, SSPA, topGO, xcms Package: MVCClass Version: 1.32.0 Depends: R (>= 2.1.0), methods License: LGPL Title: Model-View-Controller (MVC) Classes Description: Creates classes used in model-view-controller (MVC) design biocViews: Visualization, Infrastructure, GraphsAndNetworks Author: Elizabeth Whalen Maintainer: Elizabeth Whalen MD5sum: d929e3a7dd3a4754a6389ae87c8b0cf7 source.ver: src/contrib/MVCClass_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MVCClass_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MVCClass_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MVCClass_1.32.0.tgz vignettes: vignettes/MVCClass/inst/doc/MVCClass.pdf vignetteTitles: MVCClass hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MVCClass/inst/doc/MVCClass.R dependsOnMe: BioMVCClass Package: mzR Version: 1.4.7 Depends: Rcpp (>= 0.10.3), methods, utils Imports: Biobase LinkingTo: Rcpp Suggests: msdata (>= 0.1.9), RUnit, faahKO License: Artistic-2.0 Archs: i386, x64 Title: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data) Description: mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML. The netCDF reading code has previously been used in XCMS. biocViews: Infrastructure, Bioinformatics, DataImport, Proteomics, Metabolomics, MassSpectrometry Author: Bernd Fischer, Steffen Neumann, Laurent Gatto Maintainer: Bernd Fischer , Steffen Neumann , Laurent Gatto SystemRequirements: GNU make, NetCDF, zlib MD5sum: 9890c907c767e81709abd5268a3c2eb6 source.ver: src/contrib/mzR_1.4.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/mzR_1.4.7.zip win64.binary.ver: bin/windows64/contrib/2.15/mzR_1.4.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mzR_1.4.7.tgz vignettes: vignettes/mzR/inst/doc/mzR.pdf vignetteTitles: mzR,, Ramp,, mzXML,, mzData,, mzML hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mzR/inst/doc/mzR.R dependsOnMe: MSnbase, TargetSearch, xcms Package: NarrowPeaks Version: 1.2.0 Depends: R (>= 2.10.0), splines Imports: GenomicRanges, IRanges, fda, CSAR Suggests: rtracklayer, GenomicRanges, CSAR License: Artistic-2.0 Archs: i386, x64 Title: Functional Principal Component Analysis to Narrow Down Transcription Factor Binding Site Candidates Description: The package processes data in wiggle track format (WIG) commonly produced by several ChIP-seq data analysis tools by applying functional version of principal component analysis (FPCA) over a set of selected candidate enriched regions. This is done in order to shorten the genomic locations accounting for a given proportion of variation among the enrichment-score profiles. It allows the user to discriminate between binding regions in close proximity to each other and to narrow down the length of the putative transcription factor binding sites while preserving the information present in the variability of the dataset and capturing major sources of variation. biocViews: Visualization, ChIPseq, Transcription, Genetics Author: Pedro Madrigal , with contributions from Pawel Krajewski Maintainer: Pedro Madrigal MD5sum: 284ddff63b3733ca9c2d848fafda315c source.ver: src/contrib/NarrowPeaks_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NarrowPeaks_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NarrowPeaks_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NarrowPeaks_1.2.0.tgz vignettes: vignettes/NarrowPeaks/inst/doc/NarrowPeaks.pdf vignetteTitles: NarrowPeaks Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NarrowPeaks/inst/doc/NarrowPeaks.R Package: ncdfFlow Version: 1.4.3 Depends: R (>= 2.14.0), flowCore Imports: Biobase,flowCore,flowViz,methods License: Artistic-2.0 Title: ncdfFlow: A package that provides ncdf based storage for flow cytometry data. Description: Provides netCDF storage based methods and functions for manipulation of flow cytometry data. biocViews: FlowCytometry Author: Mike Jiang,Greg Finak,N. Gopalakrishnan Maintainer: M. Jiang SystemRequirements: netcdf 4.0.1, hdf5 MD5sum: c1eb7ca1817369c5f94b89b6b63c9340 source.ver: src/contrib/ncdfFlow_1.4.3.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ncdfFlow_1.4.3.tgz vignettes: vignettes/ncdfFlow/inst/doc/ncdfFlow.pdf vignetteTitles: Basic Functions for Flow Cytometry Data hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ncdfFlow/inst/doc/ncdfFlow.R Package: NCIgraph Version: 1.6.0 Depends: graph, R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCytoscape, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 Title: Pathways from the NCI Pathways Database Description: Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them. biocViews: Pathways, GraphsAndNetworks Author: Laurent Jacob Maintainer: Laurent Jacob MD5sum: 7b391fc3851573659b5164c2c48d718a source.ver: src/contrib/NCIgraph_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NCIgraph_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NCIgraph_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NCIgraph_1.6.0.tgz vignettes: vignettes/NCIgraph/inst/doc/NCIgraph.pdf vignetteTitles: NCIgraph: networks from the NCI pathway integrated database as graphNEL objects. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NCIgraph/inst/doc/NCIgraph.R importsMe: DEGraph suggestsMe: DEGraph Package: nem Version: 2.34.0 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), plotrix, limma, cluster (>= 1.11), statmod, Hmisc, Rgraphviz Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz Suggests: Biobase (>= 1.10) Enhances: doMC, Rglpk License: GPL (>= 2) Archs: i386, x64 Title: Nested Effects Models to reconstruct phenotypic hierarchies Description: The package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) high-dimensional phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy. biocViews: Microarray, Bioinformatics, GraphsAndNetworks, Pathways Author: Holger Froehlich, Florian Markowetz, Achim Tresch, Theresa Niederberger, Christian Bender, Matthias Maneck, Claudio Lottaz, Tim Beissbarth Maintainer: Holger Froehlich URL: http://www.bioconductor.org MD5sum: bfd7efdac177dfb78edbae0261ef6d83 source.ver: src/contrib/nem_2.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/nem_2.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/nem_2.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nem_2.34.0.tgz vignettes: vignettes/nem/inst/doc/markowetz-thesis-2006.pdf, vignettes/nem/inst/doc/nem.pdf vignetteTitles: markowetz-thesis-2006.pdf, Nested Effects Models - An example in Drosophila immune response hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/nem/inst/doc/nem.R Package: netresponse Version: 1.10.0 Depends: R (>= 2.15.0), dmt, igraph0, ggplot2, graph, mclust, methods, minet, parallel, qvalue, RColorBrewer, reshape, Rgraphviz License: GPL (>=2) Archs: i386, x64 Title: NetResponse: functional network analysis Description: Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling. biocViews: CellBiology, Clustering, GeneExpression, Genetics, NetworkAnalysis, GraphsAndNetworks, DifferentialExpression, Microarray, Transcription Author: Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen Maintainer: Leo Lahti URL: http://netpro.r-forge.r-project.org/ MD5sum: e34a2d9d8d9a7ce5095a796615754b1e source.ver: src/contrib/netresponse_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/netresponse_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/netresponse_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/netresponse_1.10.0.tgz vignettes: vignettes/netresponse/inst/doc/netresponse.pdf vignetteTitles: netresponse hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/netresponse/inst/doc/netresponse.R Package: networkBMA Version: 1.0.0 Depends: R (>= 2.15.0), stats, utils, BMA License: GPL (>= 2) Title: Regression-based network inference using Bayesian Model Averaging Description: An extension of Bayesian Model Averaging (BMA) for network construction using time series gene expression data. Includes assessment functions and sample test data. Author: Chris Fraley, Ka Yee Yeung, Adrian Raftery (with contributions from Kenneth Lo and Chad Young) Maintainer: Chris Fraley MD5sum: 0eb68b2920ffc09f9c52b01f6156c05a source.ver: src/contrib/networkBMA_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/networkBMA_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/networkBMA_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/networkBMA_1.0.0.tgz vignettes: vignettes/networkBMA/inst/doc/networkBMA.pdf, vignettes/networkBMA/inst/doc/prc.pdf, vignettes/networkBMA/inst/doc/roc.pdf vignetteTitles: networkBMA, prc.pdf, roc.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/networkBMA/inst/doc/networkBMA.R Package: nnNorm Version: 2.22.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL Title: Spatial and intensity based normalization of cDNA microarray data based on robust neural nets Description: This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. biocViews: Microarray, TwoChannel, Preprocessing Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/tarca/ MD5sum: 6e28948c63eb2ae4b1136ac7dc0bccd2 source.ver: src/contrib/nnNorm_2.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/nnNorm_2.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/nnNorm_2.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nnNorm_2.22.0.tgz vignettes: vignettes/nnNorm/inst/doc/nnNormGuide.pdf, vignettes/nnNorm/inst/doc/nnNorm.pdf vignetteTitles: nnNormGuide.pdf, nnNorm Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/nnNorm/inst/doc/nnNorm.R Package: NOISeq Version: 1.1.5 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11) License: Artistic-2.0 Title: Exploratory analysis and differential expression for RNA-seq data Description: Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions. biocViews: Bioinformatics, RNAseq, DifferentialExpression, Visualization, HighThroughputSequencing Author: Sonia Tarazona, Pedro Furio-Tari, Alberto Ferrer and Ana Conesa Maintainer: Sonia Tarazona MD5sum: 190784c277c4a7aa45a7bfc7b38234f7 source.ver: src/contrib/NOISeq_1.1.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/NOISeq_1.1.5.zip win64.binary.ver: bin/windows64/contrib/2.15/NOISeq_1.1.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NOISeq_1.1.5.tgz vignettes: vignettes/NOISeq/inst/doc/NOISeq.pdf vignetteTitles: NOISeq User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NOISeq/inst/doc/NOISeq.R Package: NormqPCR Version: 1.4.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR Imports: ReadqPCR License: LGPL-3 Title: Functions for normalisation of RT-qPCR data Description: Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data. biocViews: MicrotitrePlateAssay, GeneExpression, qPCR Author: Matthias Kohl, James Perkins Maintainer: James Perkins URL: www.bioconductor.org/packages/release/bioc/html/NormqPCR.html MD5sum: 33999a4c69f90fdd23c9859837e5b133 source.ver: src/contrib/NormqPCR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NormqPCR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NormqPCR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NormqPCR_1.4.0.tgz vignettes: vignettes/NormqPCR/inst/doc/NormqPCR.pdf vignetteTitles: NormqPCR: Functions for normalisation of RT-qPCR data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NormqPCR/inst/doc/NormqPCR.R Package: NTW Version: 1.8.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 Title: Predict gene network using an Ordinary Differential Equation (ODE) based method Description: This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method. biocViews: Preprocessing Author: Wei Xiao, Yin Jin, Darong Lai, Xinyi Yang, Yuanhua Liu, Christine Nardini Maintainer: Yuanhua Liu MD5sum: c23fb57ab88ac5cf0bde2a1f8c993f1a source.ver: src/contrib/NTW_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NTW_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NTW_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NTW_1.8.0.tgz vignettes: vignettes/NTW/inst/doc/NTW.pdf vignetteTitles: NTW vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NTW/inst/doc/NTW.R Package: nucleR Version: 1.6.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Biobase (>= 2.15.1), ShortRead, parallel Imports: methods, BiocGenerics, IRanges, Biobase, ShortRead, GenomicRanges, stats Enhances: htSeqTools License: LGPL (>= 3) Title: Nucleosome positioning package for R Description: Nucleosome positioning for Tiling Arrays and Next Generation Sequencing Experiments biocViews: ChIPseq, Microarray, Sequencing, Genetics, HighThroughputSequencing Author: Oscar Flores, David Rossell Maintainer: Oscar Flores MD5sum: 21fd9d2d71f7d58a5667e2ee9da00ecc source.ver: src/contrib/nucleR_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/nucleR_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/nucleR_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nucleR_1.6.0.tgz vignettes: vignettes/nucleR/inst/doc/nucleR.pdf vignetteTitles: Quick analysis of nucleosome positioning experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/nucleR/inst/doc/nucleR.R Package: nudge Version: 1.24.0 Imports: stats License: GPL-2 Title: Normal Uniform Differential Gene Expression detection Description: Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample) biocViews: Microarray, TwoChannel, DifferentialExpression Author: N. Dean and A. E. Raftery Maintainer: N. Dean MD5sum: 5e97dd07e8eee406fc585f71786bce7b source.ver: src/contrib/nudge_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/nudge_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/nudge_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nudge_1.24.0.tgz vignettes: vignettes/nudge/inst/doc/nudge.vignette.pdf, vignettes/nudge/inst/doc/nvignplot1.pdf, vignettes/nudge/inst/doc/nvignplot2.pdf, vignettes/nudge/inst/doc/nvignplot3.pdf, vignettes/nudge/inst/doc/nvignplot4.pdf vignetteTitles: nudge Overview, nvignplot1.pdf, nvignplot2.pdf, nvignplot3.pdf, nvignplot4.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/nudge/inst/doc/nudge.vignette.R Package: NuPoP Version: 1.8.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Title: An R package for nucleosome positioning prediction Description: NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at http://nucleosome.stats.northwestern.edu. biocViews: Genetics,Visualization,Classification Author: Ji-Ping Wang ; Liqun Xi Maintainer: Ji-Ping Wang MD5sum: 5e415bc57603f2fb1d711d5232ca98cf source.ver: src/contrib/NuPoP_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NuPoP_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NuPoP_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NuPoP_1.8.0.tgz vignettes: vignettes/NuPoP/inst/doc/NuPoP-intro.pdf, vignettes/NuPoP/inst/doc/NuPoP-manual.pdf vignetteTitles: An R package for Nucleosome positioning prediction, NuPoP-manual.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NuPoP/inst/doc/NuPoP-intro.R Package: occugene Version: 1.18.0 Depends: R (>= 2.0.0) License: GPL (>= 2) Title: Functions for Multinomial Occupancy Distribution Description: Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries. biocViews: Bioinformatics,Annotation,Pathways Author: Oliver Will Maintainer: Oliver Will MD5sum: d2f8dfb7a98feddae574b6531ac56b78 source.ver: src/contrib/occugene_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/occugene_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/occugene_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/occugene_1.18.0.tgz vignettes: vignettes/occugene/inst/doc/occugene.pdf vignetteTitles: occugene hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/occugene/inst/doc/occugene.R Package: OCplus Version: 1.32.0 Depends: R (>= 2.1.0), akima Imports: multtest (>= 1.7.3), graphics, grDevices, stats License: LGPL Title: Operating characteristics plus sample size and local fdr for microarray experiments Description: This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). biocViews: Microarray, Bioinformatics, DifferentialExpression, MultipleComparisons Author: Yudi Pawitan and Alexander Ploner Maintainer: Alexander Ploner MD5sum: 5136e7c19d48c12c3bfe61ad455e5f79 source.ver: src/contrib/OCplus_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OCplus_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OCplus_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OCplus_1.32.0.tgz vignettes: vignettes/OCplus/inst/doc/OCplus.pdf vignetteTitles: OCplus Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OCplus/inst/doc/OCplus.R Package: oligo Version: 1.22.0 Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43), Biobase (>= 2.17.8) Imports: affyio (>= 1.25.0), affxparser (>= 1.29.11), Biostrings (>= 2.25.12), BiocGenerics (>= 0.3.2), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore (>= 1.19.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, RUnit Enhances: ff, doMC, doMPI License: LGPL (>= 2) Archs: i386, x64 Title: Preprocessing tools for oligonucleotide arrays. Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, ExonArray, GeneExpression, Bioinformatics, DataImport Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles Maintainer: Benilton Carvalho MD5sum: 3acc50248812d0826780caf817954157 source.ver: src/contrib/oligo_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/oligo_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/oligo_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/oligo_1.22.0.tgz vignettes: vignettes/oligo/inst/doc/primer.pdf vignetteTitles: oligo - Primer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/oligo/inst/doc/primer.R, vignettes/oligo/inst/doc/V1Overview.R, vignettes/oligo/inst/doc/V2NExpression.R, vignettes/oligo/inst/doc/V3AffySnpGenotype.R, vignettes/oligo/inst/doc/V4Experimental.R, vignettes/oligo/inst/doc/V5ExonGene.R dependsOnMe: ITALICS, pdInfoBuilder, SCAN.UPC, waveTiling importsMe: charm, cn.farms, frma, ITALICS suggestsMe: BiocGenerics, fastseg, frmaTools Package: oligoClasses Version: 1.20.0 Depends: R (>= 2.14), BiocGenerics (>= 0.3.2) Imports: BiocGenerics, Biobase (>= 2.17.8), methods, graphics, IRanges (>= 1.13.30), GenomicRanges, Biostrings (>= 2.23.6), affyio (>= 1.23.2), ff, foreach, BiocInstaller, utils Suggests: RSQLite, hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm, genomewidesnp5Crlmm, crlmm, SNPchip, VanillaICE, RUnit, human370v1cCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) Title: Classes for high-throughput arrays supported by oligo and crlmm Description: This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages. biocViews: Infrastructure Author: Benilton Carvalho and Robert Scharpf Maintainer: Benilton Carvalho and Robert Scharpf MD5sum: 5fde29b3b98293471a78bace36a0d4b0 source.ver: src/contrib/oligoClasses_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/oligoClasses_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/oligoClasses_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/oligoClasses_1.20.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: cn.farms, crlmm, mBPCR, oligo, waveTiling importsMe: frma, ITALICS, MinimumDistance, SNPchip, VanillaICE suggestsMe: BiocGenerics Package: OLIN Version: 1.36.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 Title: Optimized local intensity-dependent normalisation of two-color microarrays Description: Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data biocViews: Microarray, TwoChannel, QualityControl, Preprocessing, Visualization Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html MD5sum: 69c5ffe946069ae878dbd8be0f4782e5 source.ver: src/contrib/OLIN_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OLIN_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OLIN_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OLIN_1.36.0.tgz vignettes: vignettes/OLIN/inst/doc/OLIN.pdf vignetteTitles: Introduction to OLIN hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OLIN/inst/doc/OLIN.R dependsOnMe: OLINgui importsMe: OLINgui suggestsMe: maigesPack Package: OLINgui Version: 1.32.1 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 Title: Graphical user interface for OLIN Description: Graphical user interface for the OLIN package biocViews: Microarray, TwoChannel, QualityControl, Preprocessing, Visualization Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html MD5sum: 68bf48b1fcb0def62c23811203d5e5e8 source.ver: src/contrib/OLINgui_1.32.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/OLINgui_1.32.1.zip win64.binary.ver: bin/windows64/contrib/2.15/OLINgui_1.32.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OLINgui_1.32.1.tgz vignettes: vignettes/OLINgui/inst/doc/OLINgui.pdf, vignettes/OLINgui/inst/doc/OLINguiScreenshot.pdf vignetteTitles: Introduction to OLINgui, OLINguiScreenshot.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OLINgui/inst/doc/OLINgui.R Package: oneChannelGUI Version: 1.24.0 Depends: Biobase, affylmGUI, tkWidgets, IRanges, Rsamtools, Biostrings, siggenes Suggests: annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno, chipseq, BSgenome, Rgraphviz, affy ,annaffy, affyPLM, multtest, ssize, sizepower, RankProd, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, edgeR, metaArray, MergeMaid, biomaRt, GenomeGraphs,AffyCompatible, rtracklayer, Genominator, EDASeq, limma, DESeq, goseq, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, ragene10sttranscriptcluster.db, GOstats, AnnotationDbi, preprocessCore, baySeq, HuExExonProbesetLocation, MoExExonProbesetLocation, RaExExonProbesetLocation, snow, RmiR, RmiR.Hs.miRNA, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn4, R.utils, cummeRbund License: Artistic-2.0 Title: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops. Description: This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. biocViews: HighThroughputSequencing, RNAseq, Microarray, OneChannel, DataImport, QualityControl, Preprocessing, Statistics, DifferentialExpression, GUI, MultipleComparisons Author: Raffale A Calogero, Bioinformatics and Genomics Unit, Molecular Biotechnology Center, Torino (Italy) Maintainer: Raffaele A Calogero URL: http://www.bioinformatica.unito.it/oneChannelGUI/ MD5sum: f14113fa0fc8d5aeaf9e839470975f81 source.ver: src/contrib/oneChannelGUI_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/oneChannelGUI_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/oneChannelGUI_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/oneChannelGUI_1.24.0.tgz vignettes: vignettes/oneChannelGUI/inst/doc/Exon-level.analysis.pdf, vignettes/oneChannelGUI/inst/doc/fignew42.pdf, vignettes/oneChannelGUI/inst/doc/gene-level.analysis.pdf, vignettes/oneChannelGUI/inst/doc/install.pdf, vignettes/oneChannelGUI/inst/doc/RNAseq.pdf, vignettes/oneChannelGUI/inst/doc/standAloneFunctions.pdf vignetteTitles: oneChannelGUI microarray exon-level data analysis overview, fignew42.pdf, oneChannelGUI microarray gene-level data analysis overview, oneChannelGUI Installation, oneChannelGUI miRNA and RNA-seq data analysis overview, oneChannelGUI Stand Alone Functions hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/oneChannelGUI/inst/doc/Exon-level.analysis.R, vignettes/oneChannelGUI/inst/doc/gene-level.analysis.R, vignettes/oneChannelGUI/inst/doc/install.R, vignettes/oneChannelGUI/inst/doc/RNAseq.R, vignettes/oneChannelGUI/inst/doc/standAloneFunctions.R Package: ontoCAT Version: 1.10.0 Depends: rJava, methods License: Apache License 2.0 Title: Ontology traversal and search Description: The ontoCAT R package provides a simple interface to ontologies described in widely used standard formats, stored locally in the filesystem or accessible online. The full version of ontoCAT R package also supports searching for ontology terms across multiple ontologies and in major ontology repositories, as well as a number of advanced ontology navigation functions: www.ontocat.org/wiki/r biocViews: Classification, DataRepresentation Author: Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris Swertz, Misha Kapushevsky Maintainer: Natalja Kurbatova MD5sum: 4032518261701043e93c6458cd309a8e source.ver: src/contrib/ontoCAT_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ontoCAT_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ontoCAT_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ontoCAT_1.10.0.tgz vignettes: vignettes/ontoCAT/inst/doc/ontoCAT.pdf vignetteTitles: ontoCAT package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/ontoCAT/inst/doc/ontoCAT.R Package: OrderedList Version: 1.30.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2), methods Imports: Biobase, graphics, methods, stats, twilight License: GPL (>= 2) Title: Similarities of Ordered Gene Lists Description: Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. biocViews: Microarray, DifferentialExpression, MultipleComparisons Author: Xinan Yang, Stefanie Scheid, Claudio Lottaz Maintainer: Claudio Lottaz URL: http://compdiag.molgen.mpg.de/software/index.shtml MD5sum: dccdf89ec7c4cd10f8612de63342aa4d source.ver: src/contrib/OrderedList_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OrderedList_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OrderedList_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OrderedList_1.30.0.tgz vignettes: vignettes/OrderedList/inst/doc/bcb_logo.pdf, vignettes/OrderedList/inst/doc/tr_2006_01.pdf vignetteTitles: bcb_logo.pdf, Similarities of Ordered Gene Lists hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OrderedList/inst/doc/tr_2006_01.R Package: OrganismDbi Version: 1.0.3 Depends: R (>= 2.14.0), methods, AnnotationDbi (>= 1.16.10), GenomicFeatures Imports: BiocGenerics, graph, RBGL, AnnotationDbi Suggests: Homo.sapiens, Rattus.norvegicus, RUnit License: Artistic-2.0 Title: Software to enable the smooth interfacing of different database packages. Description: The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods. biocViews: AnnotationData, Infrastructure Author: Marc Carlson, Herve Pages, Martin Morgan, Valerie Obenchain Maintainer: Biocore Data Team MD5sum: aaf0ed8a361467c80349b376dfba064c source.ver: src/contrib/OrganismDbi_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/OrganismDbi_1.0.3.zip win64.binary.ver: bin/windows64/contrib/2.15/OrganismDbi_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OrganismDbi_1.0.3.tgz vignettes: vignettes/OrganismDbi/inst/doc/OrganismDbi.pdf vignetteTitles: OrganismDbi: A meta framework for Annotation Packages hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OrganismDbi/inst/doc/OrganismDbi.R Package: OSAT Version: 1.6.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 Title: OSAT: Optimal Sample Assignment Tool Description: A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. biocViews: Bioinformatics, DataRepresentation, Visualization, Design, QualityControl Author: Li Yan Maintainer: Li Yan MD5sum: 9f59187f299a07deb39632bdb789474a source.ver: src/contrib/OSAT_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OSAT_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OSAT_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OSAT_1.6.0.tgz vignettes: vignettes/OSAT/inst/doc/gSetupBlock.pdf, vignettes/OSAT/inst/doc/gSetupOptimal.pdf, vignettes/OSAT/inst/doc/Meth450_Tracking_Sheet_onepage.pdf, vignettes/OSAT/inst/doc/OSAT.pdf, vignettes/OSAT/inst/doc/paired.pdf, vignettes/OSAT/inst/doc/random.pdf vignetteTitles: gSetupBlock.pdf, gSetupOptimal.pdf, Meth450_Tracking_Sheet_onepage.pdf, An introduction to OSAT, paired.pdf, random.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OSAT/inst/doc/OSAT.R Package: OTUbase Version: 1.8.0 Depends: R (>= 2.9.0), methods, ShortRead (>= 1.4.0), Biobase, vegan Imports: Biostrings, ShortRead, IRanges License: Artistic-2.0 Title: Provides structure and functions for the analysis of OTU data Description: Provides a platform for Operational Taxonomic Unit based analysis biocViews: Bioinformatics, HighThroughputSequencingData, DataImport Author: Daniel Beck, Matt Settles, and James A. Foster Maintainer: Daniel Beck MD5sum: 6c68e316e741e951c25dcf8cb05dc54a source.ver: src/contrib/OTUbase_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OTUbase_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OTUbase_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OTUbase_1.8.0.tgz vignettes: vignettes/OTUbase/inst/doc/Introduction_to_OTUbase.pdf vignetteTitles: An introduction to OTUbase hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OTUbase/inst/doc/Introduction_to_OTUbase.R dependsOnMe: mcaGUI Package: OutlierD Version: 1.22.0 Depends: R (>= 2.3.0), Biobase, quantreg License: GPL (>= 2) Title: Outlier detection using quantile regression on the M-A scatterplots of high-throughput data Description: This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data. biocViews: Microarray, Bioinformatics Author: HyungJun Cho Maintainer: Sukwoo Kim URL: http://www.korea.ac.kr/~stat2242/ MD5sum: 37ac6251b9bd6b48cff9ec0e35d274b1 source.ver: src/contrib/OutlierD_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OutlierD_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OutlierD_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OutlierD_1.22.0.tgz vignettes: vignettes/OutlierD/inst/doc/OutlierD.pdf vignetteTitles: Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OutlierD/inst/doc/OutlierD.R Package: PADOG Version: 1.0.0 Depends: R (>= 2.14.0), KEGGdzPathwaysGEO, graphics, limma, AnnotationDbi, Biobase, methods, nlme, GSA,KEGG.db Imports: graphics, limma, hgu133plus2.db, hgu133a.db, KEGG.db, AnnotationDbi, Biobase, methods, nlme Suggests: parallel License: GPL (>= 2) Title: Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) Description: This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package. biocViews: Microarray, OneChannel, TwoChannel, Bioinformatics Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca MD5sum: 70f6f8799fbfa17eb1f4f9648b20abeb source.ver: src/contrib/PADOG_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PADOG_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PADOG_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PADOG_1.0.0.tgz vignettes: vignettes/PADOG/inst/doc/PADOG.pdf vignetteTitles: PADOG hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PADOG/inst/doc/PADOG.R Package: PAnnBuilder Version: 1.22.0 Depends: R (>= 2.7.0), methods, utils, RSQLite, Biobase (>= 1.17.0), AnnotationDbi (>= 1.3.12) Imports: methods, utils, Biobase, DBI, RSQLite, AnnotationDbi Suggests: org.Hs.ipi.db License: LGPL (>= 2.0) Title: Protein annotation data package builder Description: Processing annotation data from public data repositories and building protein-centric annotation data packages. biocViews: Annotation, Proteomics Author: Li Hong lihong@sibs.ac.cn Maintainer: Li Hong URL: http://www.biosino.org/PAnnBuilder MD5sum: d774401106a0cd7ec53ddd53788566fb source.ver: src/contrib/PAnnBuilder_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PAnnBuilder_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PAnnBuilder_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PAnnBuilder_1.22.0.tgz vignettes: vignettes/PAnnBuilder/inst/doc/fulltext.pdf, vignettes/PAnnBuilder/inst/doc/PAnnBuilder.pdf vignetteTitles: fulltext.pdf, Using the PAnnBuilder Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PAnnBuilder/inst/doc/PAnnBuilder.R Package: panp Version: 1.28.1 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) Title: Presence-Absence Calls from Negative Strand Matching Probesets Description: A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. biocViews: Infrastructure Author: Peter Warren Maintainer: Peter Warren MD5sum: 383afa151a48581e5fc0662681aa1d9f source.ver: src/contrib/panp_1.28.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/panp_1.28.1.zip win64.binary.ver: bin/windows64/contrib/2.15/panp_1.28.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/panp_1.28.1.tgz vignettes: vignettes/panp/inst/doc/panp.pdf vignetteTitles: gene presence/absence calls hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/panp/inst/doc/panp.R Package: PANR Version: 1.4.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils Suggests: snow, RedeR License: Artistic-2.0 Title: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations Description: This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects. biocViews: NetworkInference, NetworkVisualization, GraphsAndNetworks, Clustering, CellBasedAssays Author: Xin Wang Maintainer: Xin Wang MD5sum: 50b21fe6905ac0c72cebaa4f6bffb5fc source.ver: src/contrib/PANR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PANR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PANR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PANR_1.4.0.tgz vignettes: vignettes/PANR/inst/doc/fullPAN.pdf, vignettes/PANR/inst/doc/PANR-Vignette.pdf, vignettes/PANR/inst/doc/pvmodule.pdf, vignettes/PANR/inst/doc/sigmod.pdf vignetteTitles: fullPAN.pdf, Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations, pvmodule.pdf, sigmod.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PANR/inst/doc/PANR-Vignette.R, vignettes/PANR/inst/doc/PAN-Vignette.R suggestsMe: RedeR Package: parody Version: 1.16.0 Depends: R (>= 2.5.0), methods, tools, utils License: Artistic-2.0 Title: Parametric And Resistant Outlier DYtection Description: routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics biocViews: Bioinformatics, MultipleComparisons Author: VJ Carey Maintainer: VJ Carey MD5sum: f9d450191e15a7ed2b06694d5c865c22 source.ver: src/contrib/parody_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/parody_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/parody_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/parody_1.16.0.tgz vignettes: vignettes/parody/inst/doc/parody.pdf vignetteTitles: parody: parametric and resistant outlier detection hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/parody/inst/doc/parody.R dependsOnMe: arrayMvout, flowQ Package: pathRender Version: 1.26.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods Suggests: ALL, hgu95av2.db License: LGPL Title: Render molecular pathways Description: build graphs from pathway databases, render them by Rgraphviz biocViews: GraphsAndNetworks, Pathways, NetworkVisualization Author: Li Long Maintainer: Li Long URL: http://www.bioconductor.org MD5sum: 568f93542efcdccd8282d3fb4ba7bee8 source.ver: src/contrib/pathRender_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pathRender_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pathRender_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pathRender_1.26.0.tgz vignettes: vignettes/pathRender/inst/doc/pathRender.pdf, vignettes/pathRender/inst/doc/plotExG.pdf vignetteTitles: pathRender overview, pathway graphs colored by expression map hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pathRender/inst/doc/pathRender.R, vignettes/pathRender/inst/doc/plotExG.R Package: pcaGoPromoter Version: 1.2.0 Depends: R (>= 2.14.0) , ellipse Imports: Biobase (>= 2.10.0) , AnnotationDbi Suggests: Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, Biostrings, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, serumStimulation, parallel License: GPL (>= 2) Title: pcaGoPromoter is used to analyze DNA micro array data Description: This package contains functions to ease the analyses of DNA micro arrays. It utilizes principal component analysis as the initial multivariate analysis, followed by functional interpretation of the principal component dimensions with overrepresentation analysis for GO terms and regulatory interpretations using overrepresentation analysis of predicted transcription factor binding sites with the primo algorithm. biocViews: GeneExpression, Microarray, GO , Visualization Author: Morten Hansen, Jorgen Olsen Maintainer: Morten Hansen MD5sum: c4618a07df32b137795a371f61387061 source.ver: src/contrib/pcaGoPromoter_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcaGoPromoter_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pcaGoPromoter_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcaGoPromoter_1.2.0.tgz vignettes: vignettes/pcaGoPromoter/inst/doc/pcaGoPromoter.pdf vignetteTitles: pcaGoPromoter hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pcaGoPromoter/inst/doc/pcaGoPromoter.R Package: pcaMethods Version: 1.48.0 Depends: Biobase, methods, Rcpp (>= 0.8.7) Imports: BiocGenerics, MASS LinkingTo: Rcpp Suggests: matrixStats, lattice License: GPL (>= 3) Archs: i386, x64 Title: A collection of PCA methods. Description: Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany. biocViews: Bioinformatics Author: Wolfram Stacklies, Henning Redestig, Kevin Wright Maintainer: Henning Redestig SystemRequirements: Rcpp MD5sum: 629c96fd661fa7e85f0b62db9c6928f3 source.ver: src/contrib/pcaMethods_1.48.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcaMethods_1.48.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pcaMethods_1.48.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcaMethods_1.48.0.tgz vignettes: vignettes/pcaMethods/inst/doc/missingValues.pdf, vignettes/pcaMethods/inst/doc/outliers.pdf, vignettes/pcaMethods/inst/doc/pcaMethods.pdf vignetteTitles: Missing value imputation, Data with outliers, Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pcaMethods/inst/doc/missingValues.R, vignettes/pcaMethods/inst/doc/outliers.R, vignettes/pcaMethods/inst/doc/pcaMethods.R dependsOnMe: DeconRNASeq Package: pcot2 Version: 1.26.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800.db, KEGG.db, mvtnorm License: GPL (>= 2) Title: Principal Coordinates and Hotelling's T-Square method Description: PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons. biocViews: Microarray, DifferentialExpression Author: Sarah Song, Mik Black Maintainer: Sarah Song MD5sum: d91498a68d39756a11f0bfe55b9779f9 source.ver: src/contrib/pcot2_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcot2_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pcot2_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcot2_1.26.0.tgz vignettes: vignettes/pcot2/inst/doc/HowToUseGeneLocator.pdf, vignettes/pcot2/inst/doc/pcot2.pdf vignetteTitles: HowToUseGeneLocator.pdf, PCOT2 Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pcot2/inst/doc/pcot2.R Package: PCpheno Version: 1.20.0 Depends: R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats, ppiData, annotate (>= 1.17.4) Imports: AnnotationDbi, Biobase, Category, GO.db, graph, graphics, GSEABase, KEGG.db, methods, ScISI, stats, stats4 Suggests: KEGG.db, GO.db, org.Sc.sgd.db License: Artistic-2.0 Title: Phenotypes and cellular organizational units Description: Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways. biocViews: GraphsAndNetworks, Proteomics, NetworkAnalysis Author: Nolwenn Le Meur and Robert Gentleman Maintainer: Nolwenn Le Meur MD5sum: ce5603dd07b259283d426e917513821b source.ver: src/contrib/PCpheno_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PCpheno_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PCpheno_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PCpheno_1.20.0.tgz vignettes: vignettes/PCpheno/inst/doc/PCpheno.pdf vignetteTitles: PCpheno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PCpheno/inst/doc/PCpheno.R Package: pdInfoBuilder Version: 1.22.0 Depends: R (>= 2.15.0), methods, Biobase (>= 2.17.7), RSQLite (>= 0.11.1), affxparser (>= 1.29.12), oligo (>= 1.21.5) Imports: Biostrings (>= 2.25.12), IRanges (>= 1.15.44) License: Artistic-2.0 Archs: i386, x64 Title: Platform Design Information Package Builder Description: Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg. biocViews: Annotation, Infrastructure Author: Seth Falcon, Benilton Carvalho with contributions by Vince Carey, Matt Settles and Kristof de Beuf Maintainer: Benilton Carvalho MD5sum: 4dd63999ba943c11078fd15f6718ba86 source.ver: src/contrib/pdInfoBuilder_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pdInfoBuilder_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pdInfoBuilder_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pdInfoBuilder_1.22.0.tgz vignettes: vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf, vignettes/pdInfoBuilder/inst/doc/howto-AffymetrixMapping.pdf vignetteTitles: Building Annotation Packages with pdInfoBuilder for Use with the oligo Package, PDInfo Package Building Affymetrix Mapping Chips hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.R, vignettes/pdInfoBuilder/inst/doc/howto-AffymetrixMapping.R Package: pdmclass Version: 1.30.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda License: Artistic-2.0 Title: Classification of Microarray Samples using Penalized Discriminant Methods Description: This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression. biocViews: Classification Author: James W. MacDonald, Debashis Ghosh, based in part on pls code of Mike Denham Maintainer: James W. MacDonald MD5sum: e12714c49c8451292fcd9f869907436c source.ver: src/contrib/pdmclass_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pdmclass_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pdmclass_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pdmclass_1.30.0.tgz vignettes: vignettes/pdmclass/inst/doc/pdmclass.pdf vignetteTitles: pdmclass Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pdmclass/inst/doc/pdmclass.R suggestsMe: oneChannelGUI Package: PGSEA Version: 1.32.0 Depends: R (>= 2.10), GO.db, KEGG.db, AnnotationDbi, annaffy, methods, Biobase (>= 2.5.5) Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma License: GPL-2 Title: Parametric Gene Set Enrichment Analysis Description: Parametric Analysis of Gene Set Enrichment biocViews: Microarray Author: Kyle Furge and Karl Dykema Maintainer: Karl Dykema MD5sum: 27599aca3b0a2fe0e7651bf4e1d23ce9 source.ver: src/contrib/PGSEA_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PGSEA_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PGSEA_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PGSEA_1.32.0.tgz vignettes: vignettes/PGSEA/inst/doc/PGSEA2.pdf, vignettes/PGSEA/inst/doc/PGSEA.pdf vignetteTitles: HOWTO: PGSEA Example Workflow, HOWTO: PGSEA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PGSEA/inst/doc/PGSEA2.R, vignettes/PGSEA/inst/doc/PGSEA.R dependsOnMe: GeneExpressionSignature Package: pgUtils Version: 1.30.0 Depends: R (>= 1.8.0), methods, RPostgreSQL (>= 0.1) Imports: methods, RPostgreSQL (>= 0.1) License: LGPL (>= 2) Title: Utility functions for PostgreSQL databases Description: Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referential integrity and a logging mechanism. biocViews: Infrastructure Author: Johannes Rainer Maintainer: Johannes Rainer MD5sum: 0a043fc6d586a08df1a177ee68e095f4 source.ver: src/contrib/pgUtils_1.30.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pgUtils_1.30.0.tgz vignettes: vignettes/pgUtils/inst/doc/pgUtils.pdf vignetteTitles: pgUtils.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: maDB Package: phenoDist Version: 1.6.0 Depends: R (>= 2.9.0), imageHTS, e1071 Suggests: GOstats, MASS License: LGPL-2.1 Title: Phenotypic distance measures Description: PhenoDist is designed for measuring phenotypic distance in image-based high-throughput screening, in order to identify strong phenotypes and to group treatments into functional clusters. biocViews: CellBasedAssays, Bioinformatics Author: Xian Zhang, Gregoire Pau, Wolfgang Huber, Michael Boutros Maintainer: Xian Zhang URL: http://www.dkfz.de/signaling, http://www.embl.de/research/units/genome_biology/huber/ MD5sum: 59de5e43ff0ac89d88d2f6ba06053463 source.ver: src/contrib/phenoDist_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/phenoDist_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/phenoDist_1.6.0.zip vignettes: vignettes/phenoDist/inst/doc/phenoDist.pdf vignetteTitles: Introduction to phenoDist hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/phenoDist/inst/doc/phenoDist.R Package: phenoTest Version: 1.6.0 Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR Suggests: GSEABase, KEGG.db, GO.db Enhances: multicore, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>=2) Title: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation. Description: Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided. biocViews: Microarray, Bioinformatics, DifferentialExpression, MultipleComparisons, Clustering, Classification Author: Evarist Planet Maintainer: Evarist Planet MD5sum: 568ff3ba7855bb26b0f60d71b359afe3 source.ver: src/contrib/phenoTest_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/phenoTest_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/phenoTest_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/phenoTest_1.6.0.tgz vignettes: vignettes/phenoTest/inst/doc/phenoTest.pdf vignetteTitles: Manual for the phenoTest library hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/phenoTest/inst/doc/phenoTest.R Package: phyloseq Version: 1.2.1 Depends: R (>= 2.15.0), methods, ade4 (>= 1.4), ggplot2 (>= 0.9.2), picante (>= 1.3) Imports: ape (>= 3.0), foreach (>= 1.3), igraph0 (>= 0.5), multtest (>= 2.8), plyr (>= 1.7.1), reshape (>= 0.8.4), RJSONIO (>= 0.98), scales (>= 0.2.2), vegan (>= 2.0) Suggests: genefilter, testthat Enhances: doParallel (>= 1.0) License: AGPL-3 Title: Handling and analysis of high-throughput phylogenetic sequence data. Description: phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of phylogenetic sequencing data. biocViews: Clustering, Classification, MultipleComparisons, QualityControl, GeneticVariability, HighThroughputSequencing Author: Paul J. McMurdie , Susan Holmes Maintainer: Paul J. McMurdie URL: http://joey711.github.com/phyloseq/ MD5sum: 89790d32a0631672fadeb6186c661c8b source.ver: src/contrib/phyloseq_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/phyloseq_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/phyloseq_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/phyloseq_1.2.1.tgz vignettes: vignettes/phyloseq/inst/doc/phyloseq_analysis.pdf, vignettes/phyloseq/inst/doc/phyloseq_basics.pdf, vignettes/phyloseq/inst/doc/phyloseq_classes_4.pdf vignetteTitles: Analysis examples using phyloseq, Basic data manipulation using phyloseq, phyloseq_classes_4.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/phyloseq/inst/doc/phyloseq_analysis.R, vignettes/phyloseq/inst/doc/phyloseq_basics.R Package: pickgene Version: 1.30.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) Title: Adaptive Gene Picking for Microarray Expression Data Analysis Description: Functions to Analyze Microarray (Gene Expression) Data. biocViews: Microarray, DifferentialExpression Author: Brian S. Yandell Maintainer: Brian S. Yandell URL: http://www.stat.wisc.edu/~yandell/statgen MD5sum: 001227a0de1f4c136b7a5c11bb3bf827 source.ver: src/contrib/pickgene_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pickgene_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pickgene_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pickgene_1.30.0.tgz vignettes: vignettes/pickgene/inst/doc/pickgene.pdf vignetteTitles: Adaptive Gene Picking for Microarray Expression Data Analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pickgene/inst/doc/pickgene.R Package: PICS Version: 2.2.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.1.3) Imports: methods, stats4, IRanges, GenomicRanges, graphics, grDevices, stats Suggests: ShortRead, rtracklayer, parallel License: Artistic-2.0 Archs: i386, x64 Title: Probabilistic inference of ChIP-seq Description: Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. biocViews: Clustering, Visualization, Sequencing, ChIPseq Author: Xuekui Zhang , Raphael Gottardo Maintainer: Renan Sauteraud MD5sum: 04c340fd738d52394e49f9d14b4b7171 source.ver: src/contrib/PICS_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PICS_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PICS_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PICS_2.2.0.tgz vignettes: vignettes/PICS/inst/doc/PICS.pdf vignetteTitles: The PICS users guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PICS/inst/doc/PICS.R importsMe: PING Package: PING Version: 2.2.0 Depends: R(>= 2.15.0), chipseq, IRanges, GenomicRanges Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, Rsamtools Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 Archs: i386, x64 Title: Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data Description: Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. biocViews: Clustering, Statistics, Visualization, Sequencing Author: Xuekui Zhang , Raphael Gottardo , Sangsoon Woo, Maintainer: Renan Sauteraud MD5sum: fbcfc67b07fab4c6adb688d2ebe4ccb8 source.ver: src/contrib/PING_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PING_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PING_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PING_2.2.0.tgz vignettes: vignettes/PING/inst/doc/PING.pdf, vignettes/PING/inst/doc/PING-PE.pdf vignetteTitles: The PING users guide, Using PING with paired-end sequencing data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PING/inst/doc/PING-PE.R, vignettes/PING/inst/doc/PING.R Package: pint Version: 1.10.0 Depends: mvtnorm, methods, graphics, Matrix, dmt License: FreeBSD Title: Pairwise INTegration of functional genomics data Description: Pairwise data integration for functional genomics, including tools for DNA/RNA/miRNA dependency screens. biocViews: aCGH, GeneExpression, Genetics, DifferentialExpression, Microarray Author: Olli-Pekka Huovilainen and Leo Lahti Maintainer: Olli-Pekka Huovilainen MD5sum: 9ac44bcdaca68d40aeedd3e189bf9f39 source.ver: src/contrib/pint_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pint_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pint_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pint_1.10.0.tgz vignettes: vignettes/pint/inst/doc/depsearch.pdf vignetteTitles: pint hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/pint/inst/doc/depsearch.R Package: pkgDepTools Version: 1.24.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl, BiocInstaller License: GPL-2 Title: Package Dependency Tools Description: This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained. biocViews: Infrastructure, GraphsAndNetworks Author: Seth Falcon Maintainer: Seth Falcon MD5sum: 0f2feaac291f513ffd14f57961710a59 source.ver: src/contrib/pkgDepTools_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pkgDepTools_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pkgDepTools_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pkgDepTools_1.24.0.tgz vignettes: vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf vignetteTitles: How to Use pkgDepTools hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pkgDepTools/inst/doc/pkgDepTools.R Package: plateCore Version: 1.16.0 Depends: R (>= 2.10), flowCore, flowViz, lattice, latticeExtra Imports: Biobase, flowCore, graphics, grDevices, lattice, MASS, methods, robustbase, stats, utils Suggests: gplots License: Artistic-2.0 Title: Statistical tools and data structures for plate-based flow cytometry Description: Provides basic S4 data structures and routines for analyzing plate based flow cytometry data. biocViews: FlowCytometry, Infrastructure, CellBasedAssays Author: Errol Strain, Florian Hahne, and Perry Haaland Maintainer: Errol Strain URL: http://www.bioconductor.org MD5sum: d5f36acb4e3c655832868d1197a15203 source.ver: src/contrib/plateCore_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/plateCore_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/plateCore_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plateCore_1.16.0.tgz vignettes: vignettes/plateCore/inst/doc/expDens.pdf, vignettes/plateCore/inst/doc/plateCoreVig.pdf vignetteTitles: expDens.pdf, An R Package for Analysis of High Throughput Flow Cytometry Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/plateCore/inst/doc/plateCoreVig.R Package: plgem Version: 1.30.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), MASS Imports: utils License: GPL-2 Title: Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) Description: The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets. biocViews: Microarray, DifferentialExpression, Proteomics Author: Mattia Pelizzola and Norman Pavelka Maintainer: Norman Pavelka URL: http://www.genopolis.it MD5sum: 6a1d3842ac621d0b042a3413af6d7f71 source.ver: src/contrib/plgem_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/plgem_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/plgem_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plgem_1.30.0.tgz vignettes: vignettes/plgem/inst/doc/plgem.pdf vignetteTitles: An introduction to PLGEM hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/plgem/inst/doc/plgem.R Package: plier Version: 1.28.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) Archs: i386, x64 Title: Implements the Affymetrix PLIER algorithm Description: The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. biocViews: Software Author: Affymetrix Inc., Crispin J Miller, PICR Maintainer: Crispin Miller MD5sum: 7d8ca1dc5d401e03c07056399611e60e source.ver: src/contrib/plier_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/plier_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/plier_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plier_1.28.0.tgz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: virtualArray Package: PLPE Version: 1.18.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) Title: Local Pooled Error Test for Differential Expression with Paired High-throughput Data Description: This package performs tests for paired high-throughput data. biocViews: Proteomics, Microarray, DifferentialExpression Author: HyungJun Cho and Jae K. Lee Maintainer: Soo-heang Eo URL: http://www.korea.ac.kr/~stat2242/ MD5sum: 8a8958f32d4b95a3378813e9f3147625 source.ver: src/contrib/PLPE_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PLPE_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PLPE_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PLPE_1.18.0.tgz vignettes: vignettes/PLPE/inst/doc/PLPE.pdf vignetteTitles: PLPE Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PLPE/inst/doc/PLPE.R Package: plw Version: 1.18.0 Depends: R (>= 2.10), affy (>= 1.23.4) Imports: MASS, affy, graphics, splines, stats Suggests: limma License: GPL-2 Archs: i386, x64 Title: Probe level Locally moderated Weighted t-tests. Description: Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW). biocViews: Microarray, OneChannel, TwoChannel, Bioinformatics, DifferentialExpression Author: Magnus Astrand Maintainer: Magnus Astrand MD5sum: 1416b79d5832c16c8f4509070ba4aa75 source.ver: src/contrib/plw_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/plw_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/plw_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plw_1.18.0.tgz vignettes: vignettes/plw/inst/doc/HowToPLW.pdf vignetteTitles: HowTo plw hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/plw/inst/doc/HowToPLW.R Package: ppiStats Version: 1.24.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.6) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable License: Artistic-2.0 Title: Protein-Protein Interaction Statistical Package Description: Tools for the analysis of protein interaction data. biocViews: Proteomics, GraphsAndNetworks, NetworkAnalysis Author: T. Chiang and D. Scholtens with contributions from W. Huber and L. Wang Maintainer: Tony Chiang MD5sum: db0fda03dd3031dbe28aea1c079368c0 source.ver: src/contrib/ppiStats_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ppiStats_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ppiStats_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ppiStats_1.24.0.tgz vignettes: vignettes/ppiStats/inst/doc/ppiStats.pdf vignetteTitles: ppiStats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ppiStats/inst/doc/ppiStats.R dependsOnMe: PCpheno suggestsMe: BiocCaseStudies, RpsiXML Package: prada Version: 1.34.0 Depends: R (>= 2.10.0), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, BiocGenerics, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, stats4, utils Suggests: cellHTS, tcltk License: LGPL Archs: i386, x64 Title: Data analysis for cell-based functional assays Description: Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy). biocViews: CellBasedAssays, Visualization Author: Florian Hahne , Wolfgang Huber , Markus Ruschhaupt, Joern Toedling Maintainer: Florian Hahne URL: http://www.dkfz.de/mga/whuber, http://www.dkfz.de/LIFEdb MD5sum: 59767f81cdbf84dafc9163bbd2633544 source.ver: src/contrib/prada_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/prada_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/prada_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/prada_1.34.0.tgz vignettes: vignettes/prada/inst/doc/norm2.pdf, vignettes/prada/inst/doc/prada2cellHTS.pdf vignetteTitles: Removal of contaminants from FACS data, Combining prada output and cellHTS hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prada/inst/doc/norm2.R, vignettes/prada/inst/doc/prada2cellHTS.R htmlDocs: vignettes/prada/inst/doc/fcs3.html dependsOnMe: cellHTS, domainsignatures, RNAither importsMe: cellHTS2 Package: PREDA Version: 1.4.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, samr, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 Title: Position RElated Data Anlysis Description: Package for the position related analysis of quantitative functional genomics data. biocViews: Software, CopyNumberVariants, GeneExpression, Genetics Author: Francesco Ferrari Maintainer: Francesco Ferrari MD5sum: 00b67fbef31ff576597e3d1d63243c81 source.ver: src/contrib/PREDA_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PREDA_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PREDA_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PREDA_1.4.0.tgz vignettes: vignettes/PREDA/inst/doc/PREDAclasses.pdf, vignettes/PREDA/inst/doc/PREDAtutorial.pdf vignetteTitles: PREDA S4-classes, PREDA tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PREDA/inst/doc/PREDAclasses.R, vignettes/PREDA/inst/doc/PREDAtutorial.R Package: predictionet Version: 1.4.0 Depends: igraph0, catnet Imports: penalized, RBGL, MASS Suggests: network, minet, knitr License: Artistic-2.0 Title: Inference for predictive networks designed for (but not limited to) genomic data Description: This package contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases. The main function is able to generate networks using Bayesian or regression-based inference methods; while the former is limited to < 100 of variables, the latter may infer networks with hundreds of variables. Several statistics at the edge and node levels have been implemented (edge stability, predictive ability of each node, ...) in order to help the user to focus on high quality subnetworks. Ultimately, this package is used in the 'Predictive Networks' web application developed by the Dana-Farber Cancer Institute in collaboration with Entagen. biocViews: GraphsAndNetworks, NetworkInference Author: Benjamin Haibe-Kains, Catharina Olsen, Gianluca Bontempi, John Quackenbush Maintainer: Benjamin Haibe-Kains , Catharina Olsen URL: http://compbio.dfci.harvard.edu, http://www.ulb.ac.be/di/mlg MD5sum: f5b0e11b149158b1f4418ef0c0af5205 source.ver: src/contrib/predictionet_1.4.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/predictionet_1.4.0.tgz vignettes: vignettes/predictionet/inst/doc/predictionet-boxplotr2pwcvfig2.pdf, vignettes/predictionet/inst/doc/predictionet-boxplotstabpwcvfig2.pdf, vignettes/predictionet/inst/doc/predictionet-cytoscape.pdf, vignettes/predictionet/inst/doc/predictionet-edgecoldiffig.pdf, vignettes/predictionet/inst/doc/predictionet-edgestabfig.pdf, vignettes/predictionet/inst/doc/predictionet-genepredabmccfig.pdf, vignettes/predictionet/inst/doc/predictionet-genepredabmcctestfig.pdf, vignettes/predictionet/inst/doc/predictionet-genepredabr2fig.pdf, vignettes/predictionet/inst/doc/predictionet-genepredabr2testfig.pdf, vignettes/predictionet/inst/doc/predictionet.pdf, vignettes/predictionet/inst/doc/predictionet-pn_webapp_ras.pdf, vignettes/predictionet/inst/doc/predictionet-regnetcvpriorsweightfig2.pdf, vignettes/predictionet/inst/doc/predictionet-regnetcvtopo1topo2fig2.pdf, vignettes/predictionet/inst/doc/predictionet-regnetcvtopo1topo2predfig2.pdf, vignettes/predictionet/inst/doc/predictionet-regnetcvtopo1topo2stabfig2.pdf, vignettes/predictionet/inst/doc/predictionet-regrnet_design.pdf, vignettes/predictionet/inst/doc/predictionet-regrnetopofig.pdf vignetteTitles: predictionet-boxplotr2pwcvfig2.pdf, predictionet-boxplotstabpwcvfig2.pdf, predictionet-cytoscape.pdf, predictionet-edgecoldiffig.pdf, predictionet-edgestabfig.pdf, predictionet-genepredabmccfig.pdf, predictionet-genepredabmcctestfig.pdf, predictionet-genepredabr2fig.pdf, predictionet-genepredabr2testfig.pdf, predictionet, predictionet-pn_webapp_ras.pdf, predictionet-regnetcvpriorsweightfig2.pdf, predictionet-regnetcvtopo1topo2fig2.pdf, predictionet-regnetcvtopo1topo2predfig2.pdf, predictionet-regnetcvtopo1topo2stabfig2.pdf, predictionet-regrnet_design.pdf, predictionet-regrnetopofig.pdf hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/predictionet/inst/doc/predictionet.R Package: preprocessCore Version: 1.20.0 Depends: methods Imports: stats License: LGPL (>= 2) Archs: i386, x64 Title: A collection of pre-processing functions Description: A library of core preprocessing routines biocViews: Infrastructure Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad MD5sum: b52c0a508ab4a3c148b925b4525f74a8 source.ver: src/contrib/preprocessCore_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/preprocessCore_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/preprocessCore_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/preprocessCore_1.20.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: affyPLM, cqn, crlmm, RefPlus, virtualArray importsMe: affy, AffyTiling, charm, cn.farms, frma, frmaTools, lumi, MBCB, minfi, MSnbase, oligo, waveTiling suggestsMe: oneChannelGUI Package: PROcess Version: 1.34.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 Title: Ciphergen SELDI-TOF Processing Description: A package for processing protein mass spectrometry data. biocViews: MassSpectrometry, Proteomics Author: Xiaochun Li Maintainer: Xiaochun Li MD5sum: fb423b67ec7c5d7ae0d9a36fd505b288 source.ver: src/contrib/PROcess_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PROcess_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PROcess_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PROcess_1.34.0.tgz vignettes: vignettes/PROcess/inst/doc/howtoprocess.pdf vignetteTitles: HOWTO PROcess hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PROcess/inst/doc/howtoprocess.R Package: procoil Version: 1.8.0 Depends: R (>= 2.10.1), methods Imports: methods, stats, graphics, utils Suggests: Biostrings License: GPL (>= 2) Title: Prediction of Oligomerization of Coiled Coil Proteins Description: The procoil package allows to predict whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. The predict function not only computes the prediction itself, but also a profile which allows to determine the strengths to which the individual residues are indicative for either class. Profiles can also be plotted and exported to files. biocViews: Proteomics, Classification Author: Ulrich Bodenhofer Maintainer: Ulrich Bodenhofer URL: http://www.bioinf.jku.at/software/procoil/ MD5sum: 72b2e6a3777e1612b0f43a2be3b6d035 source.ver: src/contrib/procoil_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/procoil_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/procoil_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/procoil_1.8.0.tgz vignettes: vignettes/procoil/inst/doc/procoil.pdf vignetteTitles: PrOCoil - A Web Service and an R Package for Predicting the Oligomerization of Coiled-Coil Proteins hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/procoil/inst/doc/procoil.R Package: PROMISE Version: 1.10.0 Depends: R (>= 2.11.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) Title: PRojection Onto the Most Interesting Statistical Evidence Description: A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019 biocViews: Microarray, OneChannel, Bioinformatics, MultipleComparisons, GeneExpression Author: Stan Pounds , Xueyuan Cao Maintainer: Stan Pounds , Xueyuan Cao MD5sum: 464bae33ad8d6e0fc3af34ef453322ce source.ver: src/contrib/PROMISE_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PROMISE_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PROMISE_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PROMISE_1.10.0.tgz vignettes: vignettes/PROMISE/inst/doc/PROMISE.pdf vignetteTitles: An introduction to PROMISE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PROMISE/inst/doc/PROMISE.R Package: puma Version: 3.0.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.23.4), graphics, grDevices, methods, stats, utils, mclust Imports: Biobase (>= 2.5.5), affy (>= 1.23.4) Suggests: pumadata, affydata, snow, limma, annotate, ROCR License: LGPL Archs: i386, x64 Title: Propagating Uncertainty in Microarray Analysis Description: Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions. biocViews: Microarray, OneChannel, Preprocessing, Bioinformatics, DifferentialExpression, Clustering Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti, Li Zhang Maintainer: Richard Pearson URL: http://umber.sbs.man.ac.uk/resources/puma MD5sum: 1a671edcd1062cbab611831698064302 source.ver: src/contrib/puma_3.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/puma_3.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/puma_3.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/puma_3.0.0.tgz vignettes: vignettes/puma/inst/doc/puma-014.pdf, vignettes/puma/inst/doc/puma-015.pdf, vignettes/puma/inst/doc/puma-016.pdf, vignettes/puma/inst/doc/puma-022.pdf, vignettes/puma/inst/doc/puma-023.pdf, vignettes/puma/inst/doc/puma-024.pdf, vignettes/puma/inst/doc/puma.pdf vignetteTitles: puma-014.pdf, puma-015.pdf, puma-016.pdf, puma-022.pdf, puma-023.pdf, puma-024.pdf, puma.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: tigre suggestsMe: tigre Package: pvac Version: 1.6.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) Title: PCA-based gene filtering for Affymetrix arrays Description: The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC). biocViews: Bioinformatics, Microarray, OneChannel, QualityControl Author: Jun Lu and Pierre R. Bushel Maintainer: Jun Lu , Pierre R. Bushel MD5sum: a8def8f89aed67c11078379b09357603 source.ver: src/contrib/pvac_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pvac_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pvac_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pvac_1.6.0.tgz vignettes: vignettes/pvac/inst/doc/density.pdf, vignettes/pvac/inst/doc/pvac.pdf vignetteTitles: density.pdf, PCA-based gene filtering for Affymetrix GeneChips hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pvac/inst/doc/pvac.R Package: PWMEnrich Version: 1.2.0 Depends: methods, Biostrings, grid Imports: seqLogo, gdata, evd Suggests: BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel License: GPL-3 Title: PWM enrichment analysis Description: Asses the enrichment of already known PWMs (e.g. from JASPAR) in DNA sequences. Motif hits in a sequence or DNA region are considered together and P-values derived for their joint pattern. The package implements multiple algorithms, including fixed-threshold (Z-score) and threshold-free (Lognormal normalization and Clover) methods. The main goal is to identify a set of transcription factors that most likely bind to a single sequence, group of sequences, or show significantly different binding affinity between two sets of sequences. biocViews: Bioinformatics, SequenceMatching Author: Robert Stojnic Maintainer: Robert Stojnic MD5sum: 7016dd8acac0ab5c153f9f06cc8d5155 source.ver: src/contrib/PWMEnrich_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PWMEnrich_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PWMEnrich_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PWMEnrich_1.2.0.tgz vignettes: vignettes/PWMEnrich/inst/doc/PWMEnrich.pdf vignetteTitles: Overview of the 'PWMEnrich' package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PWMEnrich/inst/doc/PWMEnrich.R Package: qpcrNorm Version: 1.16.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) Title: Data-driven normalization strategies for high-throughput qPCR data. Description: The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. biocViews: Preprocessing, GeneExpression Author: Jessica Mar Maintainer: Jessica Mar MD5sum: c6aa1ef197643c05eae377031150d495 source.ver: src/contrib/qpcrNorm_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/qpcrNorm_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/qpcrNorm_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qpcrNorm_1.16.0.tgz vignettes: vignettes/qpcrNorm/inst/doc/qpcrNorm.pdf vignetteTitles: qPCR Normalization Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qpcrNorm/inst/doc/qpcrNorm.R suggestsMe: EasyqpcR Package: qpgraph Version: 1.14.4 Depends: R (>= 2.10), methods Imports: methods, annotate, Matrix, graph, Biobase, GGBase, AnnotationDbi Suggests: Matrix, mvtnorm, graph, genefilter, Category, org.EcK12.eg.db, GOstats Enhances: rlecuyer, snow, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Title: Reverse engineering of molecular regulatory networks with qp-graphs Description: q-order partial correlation graphs, or qp-graphs for short, are undirected Gaussian graphical Markov models built from q-order partial correlations. They are useful for learning undirected graphical Gaussian Markov models from data sets where the number of random variables p exceeds the available sample size n as, for instance, in the case of microarray data where they can be employed to reverse engineer a molecular regulatory network. biocViews: Microarray, GeneExpression, Transcription, Pathways, NetworkInference, GraphsAndNetworks, GeneRegulation Author: R. Castelo and A. Roverato Maintainer: Robert Castelo URL: http://functionalgenomics.upf.edu/qpgraph MD5sum: 25d37d01a74fa8bbbb1fc82fb2d9255d source.ver: src/contrib/qpgraph_1.14.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/qpgraph_1.14.4.zip win64.binary.ver: bin/windows64/contrib/2.15/qpgraph_1.14.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qpgraph_1.14.4.tgz vignettes: vignettes/qpgraph/inst/doc/BasicUsersGuide.pdf, vignettes/qpgraph/inst/doc/qpTxRegNet.pdf vignetteTitles: BasicUsersGuide.pdf, Reverse-engineer transcriptional regulatory networks using qpgraph hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qpgraph/inst/doc/qpTxRegNet.R Package: qrqc Version: 1.12.0 Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable, Rsamtools (>= 1.3.28), testthat Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats LinkingTo: Rsamtools License: GPL (>=2) Archs: i386, x64 Title: Quick Read Quality Control Description: Quickly scans reads and gathers statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected. biocViews: Sequencing, QualityControl, DataImport, Preprocessing, Visualization, HighThroughputSequencing Author: Vince Buffalo Maintainer: Vince Buffalo URL: http://github.com/vsbuffalo/qrqc MD5sum: 738349207336256b6e3b87b9c6f168d9 source.ver: src/contrib/qrqc_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/qrqc_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/qrqc_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qrqc_1.12.0.tgz vignettes: vignettes/qrqc/inst/doc/qrqc.pdf vignetteTitles: Using the qrqc package to gather information about sequence qualities hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qrqc/inst/doc/qrqc.R Package: QUALIFIER Version: 1.2.0 Depends: R (>= 2.14.0),reshape,flowWorkspace,flowViz,flowCore,RColorBrewer Imports: MASS,hwriter,RSVGTipsDevice,lattice,stats4,flowCore,flowViz,methods,flowWorkspace,reshape Enhances: ncdfFlow License: Artistic-2.0 Title: Qualitiy Control of Gated Flow Cytometry Experiments Description: Provides quality control and quality assessment tools for gated flow cytometry data. biocViews: Infrastructure, Flowcytometry, CellBasedAssays Author: Mike Jiang,Greg Finak,Raphael Gottardo Maintainer: Mike Jiang MD5sum: 7df1b07a9a838988eb6d3642165298f5 source.ver: src/contrib/QUALIFIER_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/QUALIFIER_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/QUALIFIER_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/QUALIFIER_1.2.0.tgz vignettes: vignettes/QUALIFIER/inst/doc/QUALIFIER.pdf vignetteTitles: Quality assessment for gated Flow Cytometry Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/QUALIFIER/inst/doc/QUALIFIER.R Package: quantsmooth Version: 1.24.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 Title: Quantile smoothing and genomic visualization of array data Description: Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53. biocViews: Visualization, CopyNumberVariants Author: Jan Oosting, Paul Eilers, Renee Menezes Maintainer: Jan Oosting MD5sum: e2d82df1c3adf2fb35415b0cc8480e31 source.ver: src/contrib/quantsmooth_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/quantsmooth_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/quantsmooth_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/quantsmooth_1.24.0.tgz vignettes: vignettes/quantsmooth/inst/doc/quantsmooth.pdf vignetteTitles: quantsmooth hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/quantsmooth/inst/doc/quantsmooth.R dependsOnMe: beadarraySNP importsMe: GWASTools, SIM suggestsMe: PREDA Package: qvalue Version: 1.32.0 Imports: graphics, grDevices, stats, tcltk License: LGPL Title: Q-value estimation for false discovery rate control Description: This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. biocViews: MultipleComparisons Author: Alan Dabney and John D. Storey , with assistance from Gregory R. Warnes Maintainer: John D. Storey MD5sum: 26b6e5571d2b884f38160dc14897c9e6 source.ver: src/contrib/qvalue_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/qvalue_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/qvalue_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qvalue_1.32.0.tgz vignettes: vignettes/qvalue/inst/doc/manual.pdf, vignettes/qvalue/inst/doc/pHist.pdf, vignettes/qvalue/inst/doc/qHist.pdf, vignettes/qvalue/inst/doc/qPlots.pdf, vignettes/qvalue/inst/doc/qvalue.pdf vignetteTitles: manual.pdf, pHist.pdf, qHist.pdf, qPlots.pdf, qvalue Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qvalue/inst/doc/qvalue.R dependsOnMe: anota, CancerMutationAnalysis, DEGseq, netresponse, SSPA, webbioc importsMe: anota, DOSE, ReactomePA, synapter, trigger, webbioc suggestsMe: LBE, maanova, PREDA Package: r3Cseq Version: 1.4.0 Depends: R (>= 2.14.0), IRanges, BSgenome,ShortRead, rtracklayer, RColorBrewer, methods Suggests: BSgenome.Mmusculus.UCSC.mm9 License: GPL-3 Title: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) Description: This package is an implementation of data analysis for the long-range interactions from 3C-seq assay. biocViews: Preprocessing, Sequencing, HighThroughputSequencing, Author: Supat Thongjuea, Bergen Center for Computational Science, Norway Maintainer: Supat Thongjuea MD5sum: 816dd54acfe2aba2b3169ee99b4ed7a9 source.ver: src/contrib/r3Cseq_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/r3Cseq_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/r3Cseq_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/r3Cseq_1.4.0.tgz vignettes: vignettes/r3Cseq/inst/doc/r3Cseq.pdf vignetteTitles: r3Cseq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/r3Cseq/inst/doc/r3Cseq.R Package: R453Plus1Toolbox Version: 1.8.1 Depends: R (>= 2.12.0), BiocGenerics, Biobase, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer2,TeachingDemos Imports: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), biomaRt, Biostrings, BSgenome, IRanges (>= 1.13.10), methods, R2HTML, Rsamtools, rtracklayer, ShortRead, VariantAnnotation Suggests: rtracklayer, ShortRead, Rsamtools, BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Archs: i386, x64 Title: A package for importing and analyzing data from Roche's Genome Sequencer System. Description: The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided. biocViews: HighThroughputSequencing, Infrastructure, DataImport, DataRepresentation, Visualization, QualityControl, ReportWriting Author: Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert Maintainer: Hans-Ulrich Klein MD5sum: 8ba8df3f10abba6ed2a82265da4dc5f0 source.ver: src/contrib/R453Plus1Toolbox_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/R453Plus1Toolbox_1.8.1.zip win64.binary.ver: bin/windows64/contrib/2.15/R453Plus1Toolbox_1.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/R453Plus1Toolbox_1.8.1.tgz vignettes: vignettes/R453Plus1Toolbox/inst/doc/vignette.pdf vignetteTitles: A package for importing and analyzing data from Roche's Genome Sequencer System hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/R453Plus1Toolbox/inst/doc/vignette.R Package: rama Version: 1.32.0 Depends: R(>= 2.5.0) License: GPL (>= 2) Archs: i386, x64 Title: Robust Analysis of MicroArrays Description: Robust estimation of cDNA microarray intensities with replicates. The package uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance. biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Raphael Gottardo Maintainer: Raphael Gottardo MD5sum: 58f85db6c04a5716fd3f8ea6fb45b1c3 source.ver: src/contrib/rama_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rama_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rama_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rama_1.32.0.tgz vignettes: vignettes/rama/inst/doc/rama.pdf vignetteTitles: rama Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rama/inst/doc/rama.R dependsOnMe: bridge Package: RamiGO Version: 1.4.0 Depends: gsubfn,methods Imports: igraph,RCurl,png,RCytoscape,graph License: Artistic-2.0 Title: AmiGO visualize R interface Description: R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. biocViews: GO, NetworkVisualization, GraphsAndNetworks, Classification, ConnectTools Author: Markus Schroeder, Daniel Gusenleitner, John Quackenbush, Aedin Culhane, Benjamin Haibe-Kains Maintainer: Markus Schroeder MD5sum: 76e8783ef58723c0b94494f063e874ce source.ver: src/contrib/RamiGO_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RamiGO_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RamiGO_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RamiGO_1.4.0.tgz vignettes: vignettes/RamiGO/inst/doc/RamiGO.pdf vignetteTitles: RamiGO: An Introduction (HowTo) hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RamiGO/inst/doc/RamiGO.R Package: randPack Version: 1.4.0 Depends: methods Imports: Biobase License: Artistic 2.0 Title: Randomization routines for Clinical Trials Description: A suite of classes and functions for randomizing patients in clinical trials. biocViews: Statistics Author: Vincent Carey and Robert Gentleman Maintainer: Robert Gentleman MD5sum: e75f8691683e237ccf0f4da191dadc7d source.ver: src/contrib/randPack_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/randPack_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/randPack_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/randPack_1.4.0.tgz vignettes: vignettes/randPack/inst/doc/randPack.pdf vignetteTitles: Clinical trial randomization infrastructure hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/randPack/inst/doc/randPack.R Package: RankProd Version: 2.30.0 Depends: R (>= 1.9.0) Imports: graphics License: file LICENSE Title: Rank Product method for identifying differentially expressed genes with application in meta-analysis Description: Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification. biocViews: DifferentialExpression Author: Fangxin Hong and Ben Wittner with contribution from Rainer Breitling , Colin Smith , and Florian Battke Maintainer: Fangxin Hong MD5sum: a471628af2591dd0fd0398fad4b9ea39 source.ver: src/contrib/RankProd_2.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RankProd_2.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RankProd_2.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RankProd_2.30.0.tgz vignettes: vignettes/RankProd/inst/doc/RankProd.pdf vignetteTitles: RankProd Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/RankProd/inst/doc/RankProd.R dependsOnMe: RNAither importsMe: HTSanalyzeR suggestsMe: oneChannelGUI Package: RbcBook1 Version: 1.26.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 Title: Support for Springer monograph on Bioconductor Description: tools for building book biocViews: Software Author: Vince Carey and Wolfgang Huber Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey MD5sum: 2c91fd0bf80a236000600469531dc6b6 source.ver: src/contrib/RbcBook1_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RbcBook1_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RbcBook1_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RbcBook1_1.26.0.tgz vignettes: vignettes/RbcBook1/inst/doc/RbcBook1.pdf vignetteTitles: RbcBook1 Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RbcBook1/inst/doc/RbcBook1.R Package: RBGL Version: 1.34.0 Depends: graph, methods Imports: methods Suggests: Rgraphviz, XML License: Artistic-2.0 Archs: i386, x64 Title: An interface to the BOOST graph library Description: A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. biocViews: GraphsAndNetworks, NetworkAnalysis Author: Vince Carey , Li Long , R. Gentleman Maintainer: Bioconductor Package Maintainer URL: http://www.bioconductor.org MD5sum: bf928c19e200cc6cf68f0386271bedfd source.ver: src/contrib/RBGL_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RBGL_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RBGL_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RBGL_1.34.0.tgz vignettes: vignettes/RBGL/inst/doc/filedep.pdf, vignettes/RBGL/inst/doc/RBGL.pdf vignetteTitles: filedep.pdf, RBGL Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RBGL/inst/doc/RBGL.R dependsOnMe: apComplex, BioNet, CellNOptR, flowWorkspace, gene2pathway, joda, pkgDepTools, RpsiXML importsMe: biocViews, CAMERA, Category, DEGraph, GeneAnswers, GOstats, NCIgraph, nem, OrganismDbi, pkgDepTools, predictionet, Streamer suggestsMe: BiocCaseStudies, DEGraph, graph, KEGGgraph Package: RBioinf Version: 1.18.1 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Title: RBioinf Description: Functions and datasets and examples to accompany the monograph R For Bioinformatics. biocViews: GeneExpression, Microarray, Preprocessing, QualityControl, Classification, Clustering, MultipleComparison, Annotation Author: Robert Gentleman Maintainer: Robert Gentleman MD5sum: 98463365110bddedeaa53e63e0a150a7 source.ver: src/contrib/RBioinf_1.18.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/RBioinf_1.18.1.zip win64.binary.ver: bin/windows64/contrib/2.15/RBioinf_1.18.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RBioinf_1.18.1.tgz vignettes: vignettes/RBioinf/inst/doc/RBioinf.pdf vignetteTitles: RBioinf Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RBioinf/inst/doc/RBioinf.R Package: rbsurv Version: 2.16.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) Title: Robust likelihood-based survival modeling with microarray data Description: This package selects genes associated with survival. biocViews: Microarray, Bioinformatics Author: HyungJun Cho , Sukwoo Kim , Soo-heang Eo , Jaewoo Kang Maintainer: Soo-heang Eo URL: http://www.korea.ac.kr/~stat2242/ MD5sum: acbf9168b9c18a98c83a02a4154aa70d source.ver: src/contrib/rbsurv_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rbsurv_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rbsurv_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rbsurv_2.16.0.tgz vignettes: vignettes/rbsurv/inst/doc/rbsurv.pdf vignetteTitles: Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rbsurv/inst/doc/rbsurv.R Package: Rcade Version: 1.0.0 Depends: R (>= 2.14.0), methods, GenomicRanges, baySeq, Rsamtools Imports: graphics, IRanges, rgl Suggests: limma, biomaRt, RUnit, BiocGenerics License: GPL-2 Title: R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data. Description: Rcade (which stands for "R-based analysis of ChIP-seq And Differential Expression") is a tool for integrating ChIP-seq data with differential expression summary data, through a Bayesian framework. A key application is in identifing the genes targeted by a transcription factor of interest - that is, we collect genes that are associated with a ChIP-seq peak, and differential expression under some perturbation related to that TF. biocViews: DifferentialExpression, GeneExpression, Transcription, ChIPseq, Sequencing, Genetics Author: Jonathan Cairns Maintainer: Jonathan Cairns MD5sum: 258e80edd638eda0ebe5649806cefcb7 source.ver: src/contrib/Rcade_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rcade_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rcade_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rcade_1.0.0.tgz vignettes: vignettes/Rcade/inst/doc/Rcade.pdf vignetteTitles: Rcade Vignette hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Rcade/inst/doc/Rcade.R Package: RCASPAR Version: 1.4.0 License: GPL (>=3) Title: A package for survival time prediction based on a piecewise baseline hazard Cox regression model. Description: The package is the R-version of the C-based software \bold{CASPAR} (Kaderali,2006: \url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine. biocViews: aCGH, GeneExpression, Genetics, Proteomics, Visualization Author: Douaa Mugahid Maintainer: Douaa Mugahid , Lars Kaderali MD5sum: ae0fff4c0925c89e96eced8860e3eeca source.ver: src/contrib/RCASPAR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RCASPAR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RCASPAR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RCASPAR_1.4.0.tgz vignettes: vignettes/RCASPAR/inst/doc/RCASPAR.pdf vignetteTitles: RCASPAR: Software for high-dimentional-data driven survival time prediction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RCASPAR/inst/doc/RCASPAR.R Package: RchyOptimyx Version: 1.2.0 Depends: R (>= 2.10) Imports: Rgraphviz, sfsmisc, graphics, methods, graph, grDevices Suggests: flowCore, flowType License: Artistic-2.0 Archs: i386, x64 Title: Optimyzed Cellular Hierarchies for Flow Cytometry Description: Constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response). biocViews: FlowCytometry Author: Adrin Jalali, Nima Aghaeepour Maintainer: Adrin Jalali , Nima Aghaeepour MD5sum: e736ae547ae9c7d7523210bc490285e4 source.ver: src/contrib/RchyOptimyx_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RchyOptimyx_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RchyOptimyx_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RchyOptimyx_1.2.0.tgz vignettes: vignettes/RchyOptimyx/inst/doc/RchyOptimyx.pdf vignetteTitles: flowType package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RchyOptimyx/inst/doc/RchyOptimyx.R Package: RCytoscape Version: 1.8.2 Depends: R (>= 2.14.0), graph (>= 1.31.0), XMLRPC (>= 0.2.4) Imports: methods, XMLRPC, BiocGenerics Suggests: RUnit License: GPL-2 Title: Display and manipulate graphs in Cytoscape Description: Interactvive viewing and exploration of graphs, connecting R to Cytoscape. biocViews: NetworkVisualization, GraphsAndNetworks, ConnectTools Author: Paul Shannon Maintainer: Paul Shannon URL: http://rcytoscape.systemsbiology.net MD5sum: 9b743a542a01363e09fa29680f0f49c4 source.ver: src/contrib/RCytoscape_1.8.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/RCytoscape_1.8.2.zip win64.binary.ver: bin/windows64/contrib/2.15/RCytoscape_1.8.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RCytoscape_1.8.2.tgz vignettes: vignettes/RCytoscape/inst/doc/RCytoscape.pdf vignetteTitles: RCytoscape Overview hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RCytoscape/inst/doc/RCytoscape.R importsMe: categoryCompare, NCIgraph suggestsMe: GeneNetworkBuilder, graphite Package: Rdisop Version: 1.18.0 Depends: R (>= 2.0.0), RcppClassic, Rcpp LinkingTo: RcppClassic, Rcpp Suggests: RUnit License: GPL-2 Archs: i386, x64 Title: Decomposition of Isotopic Patterns Description: Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. biocViews: MassSpectrometry Author: Anton Pervukhin , Steffen Neumann Maintainer: Steffen Neumann URL: http://msbi.ipb-halle.de/ SystemRequirements: None MD5sum: d2ed19308aca11a278e02df80dd3a78c source.ver: src/contrib/Rdisop_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rdisop_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rdisop_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rdisop_1.18.0.tgz vignettes: vignettes/Rdisop/inst/doc/Rdisop.pdf vignetteTitles: Molecule Identification with Rdisop hasREADME: FALSE hasNEWS: FALSE hasINSTALL: TRUE hasLICENSE: FALSE Rfiles: vignettes/Rdisop/inst/doc/Rdisop.R suggestsMe: MSnbase Package: RDRToolbox Version: 1.8.0 Depends: R (>= 2.9.0),rgl Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) Title: A package for nonlinear dimension reduction with Isomap and LLE. Description: A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset. biocViews: Dimension,DimensionReduction,FeatureExtraction,Visualization,ClusterValidation,Microarray Author: Christoph Bartenhagen Maintainer: Christoph Bartenhagen MD5sum: 36950f7eaba5fdacb97d34051ba61cdf source.ver: src/contrib/RDRToolbox_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RDRToolbox_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RDRToolbox_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RDRToolbox_1.8.0.tgz vignettes: vignettes/RDRToolbox/inst/doc/plot3D.pdf, vignettes/RDRToolbox/inst/doc/RDRToolbox-003.pdf, vignettes/RDRToolbox/inst/doc/SwissRoll.pdf, vignettes/RDRToolbox/inst/doc/vignette.pdf vignetteTitles: plot3D.pdf, RDRToolbox-003.pdf, SwissRoll.pdf, A package for nonlinear dimension reduction with Isomap and LLE. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RDRToolbox/inst/doc/vignette.R Package: ReactomePA Version: 1.2.1 Depends: R (>= 2.10), DOSE Imports: methods, AnnotationDbi, reactome.db, stats4, plyr, igraph, qvalue, graphics Suggests: clusterProfiler, GOSemSim, org.Hs.eg.db License: GPL-2 Title: Reactome Pathway Analysis Description: This package provides functions for pathway analysis based on REACTOME pathway database. It will implement enrichment analysis, gene set enrichment analysis and functional modules detection. biocViews: Bioinformatics, Pathways, Visualization Author: Guangchuang Yu Maintainer: Guangchuang Yu MD5sum: fd7c1115bff62196f563f9cd4f21d3ff source.ver: src/contrib/ReactomePA_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/ReactomePA_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/ReactomePA_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ReactomePA_1.2.1.tgz vignettes: vignettes/ReactomePA/inst/doc/cnetplot.pdf, vignettes/ReactomePA/inst/doc/ReactomePA.pdf, vignettes/ReactomePA/inst/doc/rPAclusterProfiler.pdf vignetteTitles: cnetplot.pdf, An introduction to ReactomePA, rPAclusterProfiler.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ReactomePA/inst/doc/ReactomePA.R suggestsMe: clusterProfiler, DOSE Package: ReadqPCR Version: 1.4.0 Depends: R(>= 2.14.0), Biobase, methods, affy Imports: Biobase License: LGPL-3 Title: Read qPCR data Description: The package provides functions to read raw RT-qPCR data of different platforms. biocViews: DataImport, MicrotitrePlateAssay, GeneExpression, qPCR Author: James Perkins, Matthias Kohl Maintainer: James Perkins URL: http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html MD5sum: 806887aa162c6e48bf0cb196a726a816 source.ver: src/contrib/ReadqPCR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ReadqPCR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ReadqPCR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ReadqPCR_1.4.0.tgz vignettes: vignettes/ReadqPCR/inst/doc/ReadqPCR.pdf vignetteTitles: Functions to load RT-qPCR data into R hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ReadqPCR/inst/doc/ReadqPCR.R dependsOnMe: NormqPCR importsMe: NormqPCR Package: reb Version: 1.36.0 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) License: GPL-2 Archs: i386, x64 Title: Regional Expression Biases Description: A set of functions to dentify regional expression biases biocViews: Microarray, CopyNumberVariants, Visualization Author: Kyle A. Furge and Karl Dykema Maintainer: Karl J. Dykema MD5sum: 028bc3e685a14d3df0c9bc593dc94b27 source.ver: src/contrib/reb_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/reb_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/reb_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/reb_1.36.0.tgz vignettes: vignettes/reb/inst/doc/reb.pdf vignetteTitles: Smoothing of Microarray Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/reb/inst/doc/reb.R Package: RedeR Version: 1.6.1 Depends: R (>= 2.15), methods, igraph, RCurl, XML Imports: rJava, XMLRPC Suggests: PANR, pvclust License: GPL (>= 2) Title: Interactive visualization and manipulation of nested networks. Description: RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of modular structures, nested networks and multiple levels of hierarchical associations. It implements a callback engine by using a low-level R-to-Java interface to build and run common plugins. In this sense, RedeR takes advantage of R to run robust statistics, while the R-to-Java interface bridges the gap between network analysis and visualization. biocViews: GraphsAndNetworks, NetworkVisualization, Networks, Software, Visualization Author: Mauro Castro, Xin Wang, Florian Markowetz Maintainer: Mauro Castro URL: http://www.markowetzlab.org/software/networks.html MD5sum: 1dca5af0d388dc71e645519bf8914f04 source.ver: src/contrib/RedeR_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/RedeR_1.6.1.zip win64.binary.ver: bin/windows64/contrib/2.15/RedeR_1.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RedeR_1.6.1.tgz vignettes: vignettes/RedeR/inst/doc/fig1.pdf, vignettes/RedeR/inst/doc/fig2.pdf, vignettes/RedeR/inst/doc/fig3.pdf, vignettes/RedeR/inst/doc/fig4.pdf, vignettes/RedeR/inst/doc/fig5a.pdf, vignettes/RedeR/inst/doc/fig5b.pdf, vignettes/RedeR/inst/doc/fig5c.pdf, vignettes/RedeR/inst/doc/fig6.pdf, vignettes/RedeR/inst/doc/RedeR.pdf vignetteTitles: fig1.pdf, fig2.pdf, fig3.pdf, fig4.pdf, fig5a.pdf, fig5b.pdf, fig5c.pdf, fig6.pdf, Main vignette: RedeR Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RedeR/inst/doc/RedeR.R suggestsMe: PANR Package: REDseq Version: 1.4.0 Depends: R (>= 2.15.0), BiocGenerics (>= 0.1.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges (>= 1.13.5), multtest, stats, utils License: GPL (>=2) Title: Analysis of high-throughput sequencing data processed by restriction enzyme digestion Description: The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples. biocViews: Sequencing, SequenceMatching, Preprocessing Author: Lihua Julie Zhu and Thomas Fazzio Maintainer: Lihua Julie Zhu MD5sum: 060fc8d5cf8b7ff853cca6051e0d48ba source.ver: src/contrib/REDseq_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/REDseq_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/REDseq_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/REDseq_1.4.0.tgz vignettes: vignettes/REDseq/inst/doc/REDseq.pdf vignetteTitles: REDseq Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/REDseq/inst/doc/REDseq.R Package: RefPlus Version: 1.28.0 Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM (>= 1.18.0), preprocessCore (>= 1.4.0) Suggests: affydata License: GPL (>= 2) Title: A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. Description: The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods. biocViews: Microarray, OneChannel, Preprocessing Author: Kai-Ming Chang , Chris Harbron , Marie C South Maintainer: Kai-Ming Chang MD5sum: 36f76da73edc1c7e626f44497a39ba0e source.ver: src/contrib/RefPlus_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RefPlus_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RefPlus_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RefPlus_1.28.0.tgz vignettes: vignettes/RefPlus/inst/doc/An_Exploration_of_Extensions_to_the_RMA_Algorithm.pdf, vignettes/RefPlus/inst/doc/Extensions_to_RMA_Algorithm.pdf, vignettes/RefPlus/inst/doc/RefPlus.pdf vignetteTitles: An_Exploration_of_Extensions_to_the_RMA_Algorithm.pdf, Extensions_to_RMA_Algorithm.pdf, RefPlus Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RefPlus/inst/doc/RefPlus.R htmlDocs: vignettes/RefPlus/inst/doc/index.html Package: Repitools Version: 1.4.2 Depends: R (>= 2.13.0), methods, BiocGenerics (>= 0.1.0), GenomicRanges (>= 1.7.8) Imports: BiocGenerics, IRanges (>= 1.13.5), GenomicRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR (>= 2.99.2), DNAcopy, Ringo, aroma.affymetrix Suggests: GenomicRanges, IRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) Title: Epigenomic tools Description: Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, etc. biocViews: DNAMethylation, GeneExpression, Methylseq Author: Mark Robinson , Dario Strbenac , Aaron Statham Maintainer: Mark Robinson MD5sum: a7128fb877c1bfa482405f5edbfc9379 source.ver: src/contrib/Repitools_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/Repitools_1.4.2.zip win64.binary.ver: bin/windows64/contrib/2.15/Repitools_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Repitools_1.4.2.tgz vignettes: vignettes/Repitools/inst/doc/qc-cpgPlot.pdf, vignettes/Repitools/inst/doc/qc-enrPlot.pdf, vignettes/Repitools/inst/doc/Repitools_vignette.pdf, vignettes/Repitools/inst/doc/visualisations-binPlotsHeatmap.pdf, vignettes/Repitools/inst/doc/visualisations-binPlotsLine.pdf, vignettes/Repitools/inst/doc/visualisations-cluPlots3.pdf, vignettes/Repitools/inst/doc/visualisations-profPlots.pdf vignetteTitles: qc-cpgPlot.pdf, qc-enrPlot.pdf, Using Repitools for Epigenomic Sequencing Data, visualisations-binPlotsHeatmap.pdf, visualisations-binPlotsLine.pdf, visualisations-cluPlots3.pdf, visualisations-profPlots.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Repitools/inst/doc/Repitools_vignette.R Package: ReportingTools Version: 1.0.0 Depends: methods Imports: Biobase,hwriter,Category,GOstats,limma,lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6) Suggests: RUnit License: Artistic-2.0 Title: Tools for making reports in various formats Description: The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. biocViews: Bioinformatics, Software, Visualization, Microarray, RNAseq, GO Author: Jason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina Chaivorapol, and Josh Kaminker Maintainer: Jason A. Hackney MD5sum: afe725f98aa14450496cca83d7e1219a source.ver: src/contrib/ReportingTools_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ReportingTools_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ReportingTools_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ReportingTools_1.0.0.tgz vignettes: vignettes/ReportingTools/inst/doc/basicReportingTools.pdf, vignettes/ReportingTools/inst/doc/microarrayAnalysis.pdf, vignettes/ReportingTools/inst/doc/rnaseqAnalysis.pdf vignetteTitles: ReportingTools basics, Reporting on microarray differential expression, Reporting on RNA-seq differential expression hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ReportingTools/inst/doc/basicReportingTools.R, vignettes/ReportingTools/inst/doc/microarrayAnalysis.R, vignettes/ReportingTools/inst/doc/rnaseqAnalysis.R Package: ReQON Version: 1.4.0 Depends: R (>= 2.15.0), Rsamtools, seqbias Imports: rJava, graphics, stats, utils, grDevices License: GPL-2 Title: Recalibrating Quality Of Nucleotides Description: Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format. biocViews: Sequencing, HighThroughputSequencing, Preprocessing, QualityControl Author: Christopher Cabanski, Keary Cavin, Chris Bizon Maintainer: Christopher Cabanski SystemRequirements: Java version >= 1.6 MD5sum: e28f212d91336337db877a0ad6dd83c9 source.ver: src/contrib/ReQON_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ReQON_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ReQON_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ReQON_1.4.0.tgz vignettes: vignettes/ReQON/inst/doc/ReQON.pdf vignetteTitles: ReQON Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ReQON/inst/doc/ReQON.R Package: Resourcerer Version: 1.32.0 Depends: R (>= 1.9.0), Biobase, AnnotationDbi (>= 1.4.0) Suggests: human.db0, mouse.db0, rat.db0 License: LGPL Title: Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. Description: This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. biocViews: Annotation, Microarray Author: Jianhua Zhang Maintainer: Jianhua Zhang MD5sum: 1bfc04bd71a456989d619d9d27520aca source.ver: src/contrib/Resourcerer_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Resourcerer_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Resourcerer_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Resourcerer_1.32.0.tgz vignettes: vignettes/Resourcerer/inst/doc/Resourcerer.pdf vignetteTitles: Resourcerer Resourcerer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Resourcerer/inst/doc/Resourcerer.R Package: rGADEM Version: 2.6.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, IRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 Archs: i386, x64 Title: de novo motif discovery Description: rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software. biocViews: Microarray, ChIPchip, Sequencing, ChIPseq, GenomicSequence, MotifDiscovery Author: Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li Maintainer: Arnaud Droit MD5sum: 6fc80bc424fe9a61f54be1791d97735d source.ver: src/contrib/rGADEM_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rGADEM_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rGADEM_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rGADEM_2.6.0.tgz vignettes: vignettes/rGADEM/inst/doc/rGADEM.pdf vignetteTitles: The rGADEM users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rGADEM/inst/doc/rGADEM.R importsMe: MotIV Package: RGalaxy Version: 1.0.0 Depends: XML, methods, tools, optparse, digest Imports: BiocGenerics, Biobase, roxygen2 Suggests: RUnit, hgu95av2.db License: Artistic-2.0 Title: Make an R function available in the Galaxy web platform Description: Given an R function and its manual page, make the documented function available in Galaxy. biocViews: Infrastructure Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer MD5sum: 529123a7d22c550db249c00fde7dd80a source.ver: src/contrib/RGalaxy_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RGalaxy_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RGalaxy_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RGalaxy_1.0.0.tgz vignettes: vignettes/RGalaxy/inst/doc/RGalaxy-vignette.pdf vignetteTitles: Adding R functions to Galaxy hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RGalaxy/inst/doc/Rgalaxy-vignette.R, vignettes/RGalaxy/inst/doc/RGalaxy-vignette.R Package: Rgraphviz Version: 2.2.1 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graph, graphics, grDevices, grid, methods, utils Suggests: RUnit, BiocGenerics, XML License: file LICENSE Archs: i386, x64 Title: Provides plotting capabilities for R graph objects Description: Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. Users on all platforms must install graphviz; see the README file, available in the source distribution of this file, for details. biocViews: GraphsAndNetworks, NetworkVisualization Author: Jeff Gentry, Li Long, Robert Gentleman, Seth Falcon, Florian Hahne, Deepayan Sarkar, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen SystemRequirements: Graphviz (>= 2.16) MD5sum: dfb5ee6dd2cc11f08ef720fbf237e499 source.ver: src/contrib/Rgraphviz_2.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rgraphviz_2.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/Rgraphviz_2.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rgraphviz_2.2.1.tgz vignettes: vignettes/Rgraphviz/inst/doc/newRgraphvizInterface.pdf, vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf vignetteTitles: A New Interface to Plot Graphs Using Rgraphviz, How To Plot A Graph Using Rgraphviz hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/Rgraphviz/inst/doc/newRgraphvizInterface.R, vignettes/Rgraphviz/inst/doc/Rgraphviz.R dependsOnMe: biocGraph, BioMVCClass, flowMerge, GOFunction, hyperdraw, nem, netresponse, pathRender, TDARACNE importsMe: apComplex, biocGraph, DEGraph, GeneAnswers, GOFunction, nem, RchyOptimyx suggestsMe: altcdfenvs, annotate, BiocCaseStudies, Category, CNORfuzzy, ddgraph, DEGraph, flowCore, flowMerge, flowWorkspace, GeneNetworkBuilder, geneplotter, GlobalAncova, globaltest, GOstats, GSEABase, KEGGgraph, MLP, NCIgraph, oneChannelGUI, pcaGoPromoter, pkgDepTools, RBGL, RBioinf, Rtreemix, safe, SPIA, SRAdb, Streamer, topGO Package: rhdf5 Version: 2.2.0 Depends: methods Imports: zlibbioc License: Artistic-2.0 Archs: i386, x64 Title: HDF5 interface to R Description: This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM. biocViews: Infrastructure Author: Bernd Fischer, Gregoire Pau Maintainer: Bernd Fischer SystemRequirements: GNU make MD5sum: 15d4c2959a983106b903cd53d9c1b771 source.ver: src/contrib/rhdf5_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rhdf5_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rhdf5_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rhdf5_2.2.0.tgz vignettes: vignettes/rhdf5/inst/doc/chunksize.pdf, vignettes/rhdf5/inst/doc/rhdf5.pdf vignetteTitles: chunksize.pdf, rhdf5 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rhdf5/inst/doc/rhdf5.R, vignettes/rhdf5/inst/doc/Rhdf5.R Package: rHVDM Version: 1.24.0 Depends: R (>= 2.10), R2HTML (>= 1.5), affy (>= 1.23.4), minpack.lm (>= 1.0-5), Biobase (>= 2.5.5) License: GPL-2 Title: Hidden Variable Dynamic Modeling Description: A R implementation of HVDM (Genome Biol 2006, V7(3) R25) biocViews: Microarray, GraphsAndNetworks, Transcription, Classification, NetworkInference Author: Martino Barenco Maintainer: Martino Barenco MD5sum: 63fe98ac6a0f35e56ba20930fd8186a4 source.ver: src/contrib/rHVDM_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rHVDM_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rHVDM_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rHVDM_1.24.0.tgz vignettes: vignettes/rHVDM/inst/doc/rHVDM.pdf vignetteTitles: rHVDM primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rHVDM/inst/doc/rHVDM.R Package: Ringo Version: 1.22.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4 Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 Archs: i386, x64 Title: R Investigation of ChIP-chip Oligoarrays Description: The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities. biocViews: Microarray,TwoChannel,DataImport,QualityControl,Preprocessing Author: Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber Maintainer: J. Toedling MD5sum: cc4104c9584023f5de594dc988692fdf source.ver: src/contrib/Ringo_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Ringo_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Ringo_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Ringo_1.22.0.tgz vignettes: vignettes/Ringo/inst/doc/Ringo.pdf vignetteTitles: R Investigation of NimbleGen Oligoarrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Ringo/inst/doc/Ringo.R dependsOnMe: Starr importsMe: Repitools suggestsMe: Repitools Package: Risa Version: 1.0.0 Depends: R (>= 2.0.9), Biobase (>= 2.4.0), methods, Rcpp (>= 0.9.13) Imports: xcms Suggests: faahKO (>= 1.2.11) License: LGPL Title: Converting experimental metadata from ISA-tab into Bioconductor data structures Description: The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays. biocViews: Annotation, DataImport, MassSpectrometry Author: Alejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann, Gabriella Rustici, ISA Team Maintainer: Alejandra Gonzalez-Beltran, ISA Team URL: MD5sum: b223e3dec07f27787af4fcf50e964fc8 source.ver: src/contrib/Risa_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Risa_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Risa_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Risa_1.0.0.tgz vignettes: vignettes/Risa/inst/doc/Risa.pdf vignetteTitles: Risa: converts experimental metadata from ISA-tab into Bioconductor data structures hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Risa/inst/doc/Risa.R Package: RLMM Version: 1.20.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) Title: A Genotype Calling Algorithm for Affymetrix SNP Arrays Description: A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now. biocViews: Microarray, OneChannel, SNP, GeneticVariability Author: Nusrat Rabbee , Gary Wong Maintainer: Nusrat Rabbee URL: http://www.stat.berkeley.edu/users/nrabbee/RLMM SystemRequirements: Internal files Xba.CQV, Xba.regions (or other regions file) MD5sum: 9aa19e7b252701142b9915c7c03394d7 source.ver: src/contrib/RLMM_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RLMM_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RLMM_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RLMM_1.20.0.tgz vignettes: vignettes/RLMM/inst/doc/RLMM.pdf vignetteTitles: RLMM Doc hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RLMM/inst/doc/RLMM.R Package: Rmagpie Version: 1.14.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) Title: MicroArray Gene-expression-based Program In Error rate estimation Description: Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes. biocViews: Microarray, Classification Author: Camille Maumet , with contributions from C. Ambroise J. Zhu Maintainer: Camille Maumet URL: http://www.bioconductor.org/ MD5sum: 0adfc1374e560c9407bee605b0f6aa19 source.ver: src/contrib/Rmagpie_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rmagpie_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rmagpie_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rmagpie_1.14.0.tgz vignettes: vignettes/Rmagpie/inst/doc/Magpie_examples.pdf vignetteTitles: Rmagpie Examples hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Rmagpie/inst/doc/Magpie_examples.R Package: RMAPPER Version: 1.8.0 Depends: methods Suggests: RCurl License: Artistic 2.0 Title: R interface to the MAPPER database of transcription factor binding sites Description: The RMAPPER package allows you to retrieve a set of predicted transcription factor binding sites from the MAPPER database (http://genome.ufl.edu/mapper/) through a simple HTTP request. biocViews: Annotation, Genetics Author: VJ Carey Maintainer: Heike Sichtig , Alberto Riva MD5sum: 70eecd397096c1dc9f03620a9fe2cbb4 source.ver: src/contrib/RMAPPER_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RMAPPER_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RMAPPER_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RMAPPER_1.8.0.tgz vignettes: vignettes/RMAPPER/inst/doc/readMAPPER.pdf vignetteTitles: Interface to MAPPER TFBS database hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RMAPPER/inst/doc/readMAPPER.R Package: RMassBank Version: 1.0.0 Depends: rcdk,yaml,mzR,methods Imports: XML,RCurl Suggests: gplots,RMassBankData,xcms License: Artistic-2.0 Title: Workflow to process tandem MS files and build MassBank records Description: Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. biocViews: Bioinformatics, MassSpectrometry, Metabolomics, Software Author: Michael Stravs, Emma Schymanski Maintainer: Michael Stravs, Emma Schymanski SystemRequirements: OpenBabel MD5sum: 9bb56bcb3d3595e8249eeb70493a1224 source.ver: src/contrib/RMassBank_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RMassBank_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RMassBank_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RMassBank_1.0.0.tgz vignettes: vignettes/RMassBank/inst/doc/RMassBank.pdf vignetteTitles: RMassBank walkthrough hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RMassBank/inst/doc/RMassBank.R Package: rMAT Version: 3.8.0 Depends: R(>= 2.9.0), BiocGenerics (>= 0.1.3), IRanges (>= 1.13.10), Biobase (>= 2.15.1), affxparser Imports: stats, methods, BiocGenerics, IRanges, Biobase, affxparser, stats4 Suggests: GenomeGraphs, rtracklayer License: Artistic-2.0 Title: R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. Description: This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch! biocViews: Microarray, Preprocessing Author: Charles Cheung and Arnaud Droit and Raphael Gottardo Maintainer: Arnaud Droit and Raphael Gottardo URL: http://www.rglab.org MD5sum: 1a0da79520faa271741f37112c2e9909 source.ver: src/contrib/rMAT_3.8.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rMAT_3.8.0.tgz vignettes: vignettes/rMAT/inst/doc/rMAT.pdf vignetteTitles: The rMAT users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rMAT/inst/doc/rMAT.R Package: RmiR Version: 1.14.0 Depends: R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice Imports: DBI, methods, stats Suggests: hgug4112a.db,org.Hs.eg.db License: Artistic-2.0 Title: Package to work with miRNAs and miRNA targets with R Description: Useful functions to merge microRNA and respective targets using differents databases biocViews: Software,GeneExpression,Microarray,TimeCourse,Visualization Author: Francesco Favero Maintainer: Francesco Favero MD5sum: 0f711b8b2d583283cfe1f052a62436c4 source.ver: src/contrib/RmiR_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RmiR_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RmiR_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RmiR_1.14.0.tgz vignettes: vignettes/RmiR/inst/doc/RmiR.pdf vignetteTitles: RmiR Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RmiR/inst/doc/RmiR.R suggestsMe: oneChannelGUI Package: RNAinteract Version: 1.6.0 Depends: R (>= 2.12.0), abind, locfit, Biobase Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12) License: Artistic-2.0 Title: Estimate Pairwise Interactions from multidimensional features Description: RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis. biocViews: CellBasedAssays, QualityControl, Preprocessing, Visualization Author: Bernd Fischer Maintainer: Bernd Fischer MD5sum: 55736e53d9dde50f17377fa4ffd4f36e source.ver: src/contrib/RNAinteract_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RNAinteract_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RNAinteract_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RNAinteract_1.6.0.tgz vignettes: vignettes/RNAinteract/inst/doc/RNAinteract.pdf vignetteTitles: RNAinteract hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAinteract/inst/doc/RNAinteract.R Package: RNAither Version: 2.6.0 Depends: R (>= 2.10), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt, car, splots, methods License: Artistic-2.0 Title: Statistical analysis of high-throughput RNAi screens Description: RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes. biocViews: CellBasedAssays, QualityControl, Preprocessing, Visualization, Bioinformatics, Annotation, GO Author: Nora Rieber and Lars Kaderali, University of Heidelberg, Viroquant Research Group Modeling, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany Maintainer: Nora Rieber MD5sum: 7514f18533ffcc10b93097b009a49f84 source.ver: src/contrib/RNAither_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RNAither_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RNAither_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RNAither_2.6.0.tgz vignettes: vignettes/RNAither/inst/doc/vignetteRNAither.pdf vignetteTitles: RNAither,, an automated pipeline for the statistical analysis of high-throughput RNAi screens hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAither/inst/doc/vignetteRNAither.R Package: rnaSeqMap Version: 2.12.0 Depends: R (>= 2.11.0), methods, xmapcore, Biobase, Rsamtools Imports: GenomicRanges, IRanges, edgeR, DESeq, DBI, RMySQL (>= 0.6-0) License: GPL-2 Title: rnaSeq secondary analyses Description: The rnaSeqMap library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time biocViews: Annotation, Bioinformatics, ReportWriting, Transcription, GeneExpression, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Visualization Author: Anna Lesniewska ; Michal Okoniewski Maintainer: Michal Okoniewski MD5sum: c6459a1e233debcc2f1622e650317c8d source.ver: src/contrib/rnaSeqMap_2.12.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rnaSeqMap_2.12.0.tgz vignettes: vignettes/rnaSeqMap/inst/doc/rnaSeqMap.pdf vignetteTitles: rnaSeqMap primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rnaSeqMap/inst/doc/rnaSeqMap.R Package: ROC Version: 1.34.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase License: Artistic-2.0 Archs: i386, x64 Title: utilities for ROC, with uarray focus Description: utilities for ROC, with uarray focus biocViews: Bioinformatics, DifferentialExpression Author: Vince Carey , Henning Redestig for C++ language enhancements Maintainer: Vince Carey URL: http://www.bioconductor.org MD5sum: f316540fd92c5700b726630235b8359e source.ver: src/contrib/ROC_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ROC_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ROC_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ROC_1.34.0.tgz vignettes: vignettes/ROC/inst/doc/ROCnotes.pdf vignetteTitles: ROC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ROC/inst/doc/ROCnotes.R importsMe: clst suggestsMe: genefilter, MCRestimate Package: Rolexa Version: 1.14.0 Depends: R (>= 2.9.0), graphics, grDevices, methods, ShortRead Imports: mclust, Biostrings, graphics, grDevices, IRanges, methods, ShortRead, stats Enhances: fork License: GPL-2 Title: Statistical analysis of Solexa sequencing data Description: Provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data biocViews: Sequencing, DataImport, Preprocessing, QualityControl Author: Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef Maintainer: Jacques Rougemont MD5sum: a504b2f6a8d7e32644fafe84e6480109 source.ver: src/contrib/Rolexa_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rolexa_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rolexa_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rolexa_1.14.0.tgz vignettes: vignettes/Rolexa/inst/doc/Rolexa-vignette.pdf vignetteTitles: Rolexa hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Rolexa/inst/doc/Rolexa-vignette.R Package: rols Version: 1.0.2 Depends: methods Imports: XMLSchema (>= 0.6.0), SSOAP (>= 0.8.0), Biobase Suggests: xtable, GO.db, knitr License: GPL-2 Title: An R interface to the Ontology Lookup Service Description: This package allows to query EBI's Ontology Lookup Service (OLS) using Simple Object Access Protocol (SOAP). biocViews: Software, Annotation, MassSpectrometry, GO Author: Laurent Gatto Maintainer: Laurent Gatto URL: http://lgatto.github.com/rols/ MD5sum: 8a7605c81698fd9d90bb0ff6166e52a3 source.ver: src/contrib/rols_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/rols_1.0.2.zip win64.binary.ver: bin/windows64/contrib/2.15/rols_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rols_1.0.2.tgz vignettes: vignettes/rols/inst/doc/rols.pdf vignetteTitles: rols hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rols/inst/doc/rols.R suggestsMe: MSnbase Package: RPA Version: 1.14.0 Depends: R (>= 2.15.1), affy, affydata, methods, parallel License: FreeBSD Title: RPA: Robust Probabilistic Averaging for probe-level analysis Description: Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays. Lahti et al. "Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays", TCBB/IEEE, 2011. http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.38 biocViews: GeneExpression, Microarray, Preprocessing, QualityControl Author: Leo Lahti Maintainer: Leo Lahti MD5sum: db84efe6be234d3f78aec30c66f04c3e source.ver: src/contrib/RPA_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RPA_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RPA_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RPA_1.14.0.tgz vignettes: vignettes/RPA/inst/doc/RPA.pdf vignetteTitles: RPA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/RPA/inst/doc/RPA.R Package: RpsiXML Version: 1.18.1 Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2), AnnotationDbi Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI License: LGPL-3 Title: R interface to PSI-MI 2.5 files Description: Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously. biocViews: Infrastructure, Proteomics Author: Jitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang Maintainer: Jitao David Zhang URL: http://www.bioconductor.org MD5sum: e4ce7791ddca07a77645f0b61f75937c source.ver: src/contrib/RpsiXML_1.18.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/RpsiXML_1.18.1.zip win64.binary.ver: bin/windows64/contrib/2.15/RpsiXML_1.18.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RpsiXML_1.18.1.tgz vignettes: vignettes/RpsiXML/inst/doc/RpsiXMLApp.pdf, vignettes/RpsiXML/inst/doc/RpsiXML.pdf vignetteTitles: Application Examples of RpsiXML package, Reading PSI-25 XML files hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RpsiXML/inst/doc/RpsiXMLApp.R, vignettes/RpsiXML/inst/doc/RpsiXML.R dependsOnMe: ScISI importsMe: ScISI Package: rqubic Version: 1.4.0 Depends: methods, Biobase, biclust Imports: Biobase, biclust Suggests: RColorBrewer License: GPL-2 Archs: i386, x64 Title: Qualitative biclustering algorithm for expression data analysis in R Description: This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data. biocViews: Microarray, Clustering Author: Jitao David Zhang, with inputs from Laura Badi and Martin Ebeling Maintainer: Jitao David Zhang MD5sum: a84679abd859e7d7888499e08a998a37 source.ver: src/contrib/rqubic_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rqubic_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rqubic_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rqubic_1.4.0.tgz vignettes: vignettes/rqubic/inst/doc/rqubic.pdf vignetteTitles: Qualitative Biclustering with Bioconductor Package rqubic hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rqubic/inst/doc/rqubic.R Package: Rsamtools Version: 1.10.2 Depends: methods, IRanges (>= 1.15.35), GenomicRanges (>= 1.9.48), Biostrings (>= 2.25.6) Imports: methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc, bitops, BiocGenerics (>= 0.1.3) LinkingTo: Biostrings, IRanges Suggests: ShortRead (>= 1.13.19), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, RUnit License: Artistic-2.0 + file LICENSE Archs: i386, x64 Title: Binary alignment (BAM), variant call (BCF), or tabix file import Description: This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), binary variant call (BCF) and compressed indexed tab-delimited (tabix) files. biocViews: DataImport, Sequencing, HighThroughputSequencing Author: Martin Morgan, Herv\'e Pag\`es Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html MD5sum: 473d7bac553f2b544ebb4268f3716ce4 source.ver: src/contrib/Rsamtools_1.10.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rsamtools_1.10.2.zip win64.binary.ver: bin/windows64/contrib/2.15/Rsamtools_1.10.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rsamtools_1.10.2.tgz vignettes: vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf, vignettes/Rsamtools/inst/doc/Rsamtools-UsingCLibraries.pdf vignetteTitles: An introduction to Rsamtools, Using samtools C libraries hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/Rsamtools/inst/doc/Rsamtools-Overview.R, vignettes/Rsamtools/inst/doc/Rsamtools-UsingCLibraries.R dependsOnMe: ArrayExpressHTS, BitSeq, deepSNV, easyRNASeq, EDASeq, exomeCopy, GGtools, girafe, oneChannelGUI, qrqc, Rcade, ReQON, rnaSeqMap, ShortRead, TEQC, VariantAnnotation importsMe: annmap, ArrayExpressHTS, biovizBase, deepSNV, FunciSNP, ggbio, gmapR, HTSeqGenie, PING, R453Plus1Toolbox, rtracklayer, ShortRead, VariantAnnotation, VariantTools suggestsMe: GenomicFeatures, GenomicRanges, R453Plus1Toolbox, seqbias, Streamer Package: rsbml Version: 2.16.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 Archs: i386, x64 Title: R support for SBML, using libsbml Description: Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models. biocViews: GraphsAndNetworks, Pathways, NetworkAnalysis Author: Michael Lawrence Maintainer: Michael Lawrence URL: http://www.sbml.org SystemRequirements: libsbml (>=3.0.3) MD5sum: fafa67254298ad650f3115dd4d7d4891 source.ver: src/contrib/rsbml_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rsbml_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rsbml_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rsbml_2.16.0.tgz vignettes: vignettes/rsbml/inst/doc/quick-start.pdf vignetteTitles: Quick start for rsbml hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rsbml/inst/doc/quick-start.R Package: rSFFreader Version: 0.6.0 Depends: R (>= 2.13.0), Biostrings (>= 2.25.12), IRanges(>= 1.15.42), GenomicRanges, ShortRead(>= 1.15.9), xtable, methods Imports: methods, Biostrings, IRanges, ShortRead, GenomicRanges, Biobase LinkingTo: Biostrings, IRanges License: Artistic-2.0 Title: rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers Description: rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers. The plan is to also write out sff files and to read in flowgrams with some utils biocViews: DataImport, Sequencing, HighThroughputSequencing Author: Matt Settles , Sam Hunter, Brice Sarver, Ilia Zhbannikov, Kyu-Chul Cho Maintainer: Matt Settles MD5sum: 65958e415aba3c4b13a45e40819e8e8d source.ver: src/contrib/rSFFreader_0.6.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rSFFreader_0.6.0.tgz vignettes: vignettes/rSFFreader/inst/doc/rSFFreader.pdf vignetteTitles: An introduction to rSFFreader hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rSFFreader/inst/doc/rSFFreader.R Package: Rsubread Version: 1.8.2 License: GPL-3 Title: Rsubread: a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads Description: This package performs read mapping, exon junction detection and other tasks for next-generation sequencing data. The read mapping function implements a novel mapping paradigm based on seed-and-vote. It can be used to map both short reads and long reads (>200bp) and reads of variable lengths. It also provides functions to summarize read counts to genes or exons and gives detection p values for each gene in the RNA-seq data. biocViews: Sequencing, HighThroughputSequencing Author: Wei Shi, Yang Liao, Jenny Zhiyin Dai and Timothy Triche, Jr. Maintainer: Wei Shi URL: http://bioconductor.org/packages/release/bioc/html/Rsubread.html MD5sum: 417a9b4a0d014f42612375e473b80d8f source.ver: src/contrib/Rsubread_1.8.2.tar.gz vignettes: vignettes/Rsubread/inst/doc/Rsubread.pdf vignetteTitles: Rsubread Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Rsubread/inst/doc/Rsubread.R Package: RTCA Version: 1.10.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 Title: Open-source toolkit to analyse data from xCELLigence System (RTCA) Description: Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools. biocViews: CellBasedAssays, Infrastructure, Visualization, TimeCourse Author: Jitao David Zhang Maintainer: Jitao David Zhang URL: http://code.google.com/p/xcelligence/, http://www.xcelligence.roche.com/, http://www.nextbiomotif.com/Home/scientific-programming MD5sum: aa0ecb2d5e4750f7981afc58853317e9 source.ver: src/contrib/RTCA_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RTCA_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RTCA_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RTCA_1.10.0.tgz vignettes: vignettes/RTCA/inst/doc/aboutRTCA.pdf, vignettes/RTCA/inst/doc/RTCAtransformation.pdf vignetteTitles: Introduction to Data Analysis of the Roche xCELLigence System with RTCA Package, RTCAtransformation: Discussion of transformation methods of RTCA data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCA/inst/doc/aboutRTCA.R, vignettes/RTCA/inst/doc/RTCAtransformation.R Package: RTopper Version: 1.4.1 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db License: GPL (>= 3) Title: This package is designed to perform Gene Set Analysis across multiple genomic platforms Description: the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms. biocViews: Microarray Author: Luigi Marchionni , Svitlana Tyekucheva Maintainer: Luigi Marchionni MD5sum: 005d41fdbc5a225f0df232e4f972d669 source.ver: src/contrib/RTopper_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/RTopper_1.4.1.zip win64.binary.ver: bin/windows64/contrib/2.15/RTopper_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RTopper_1.4.1.tgz vignettes: vignettes/RTopper/inst/doc/RTopper.pdf vignetteTitles: RTopper user's manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/RTopper/inst/doc/RTopper.R Package: rtracklayer Version: 1.18.2 Depends: R (>= 2.10), methods, GenomicRanges (>= 1.9.6) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.1.0), IRanges (>= 1.15.37), GenomicRanges, Biostrings (>= 2.25.6), BSgenome (>= 1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.7.3) LinkingTo: IRanges Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db License: Artistic-2.0 Archs: i386, x64 Title: R interface to genome browsers and their annotation tracks Description: Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport. biocViews: Annotation,Visualization,DataImport Author: Michael Lawrence, Vince Carey, Robert Gentleman Maintainer: Michael Lawrence MD5sum: fc691eb429941ca2cd4fa41e2260ba03 source.ver: src/contrib/rtracklayer_1.18.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/rtracklayer_1.18.2.zip win64.binary.ver: bin/windows64/contrib/2.15/rtracklayer_1.18.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rtracklayer_1.18.2.tgz vignettes: vignettes/rtracklayer/inst/doc/rtracklayer.pdf vignetteTitles: rtracklayer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rtracklayer/inst/doc/rtracklayer.R dependsOnMe: cummeRbund, r3Cseq importsMe: ChromHeatMap, GenomicFeatures, ggbio, gmapR, Gviz, HTSeqGenie, methyAnalysis, MotifDb, R453Plus1Toolbox suggestsMe: biovizBase, GenomicFeatures, GenomicRanges, gwascat, MotIV, NarrowPeaks, oneChannelGUI, PICS, PING, R453Plus1Toolbox, Ringo, rMAT, TSSi Package: Rtreemix Version: 1.20.0 Depends: R (>= 2.5.0), methods, graph, Biobase Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL Archs: i386, x64 Title: Rtreemix: Mutagenetic trees mixture models. Description: Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc. biocViews: Bioinformatics Author: Jasmina Bogojeska Maintainer: Jasmina Bogojeska MD5sum: 817a35abca0dc903170136429b8d31f2 source.ver: src/contrib/Rtreemix_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rtreemix_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rtreemix_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rtreemix_1.20.0.tgz vignettes: vignettes/Rtreemix/inst/doc/ClassDiagram.pdf, vignettes/Rtreemix/inst/doc/ExtendedVignette.pdf, vignettes/Rtreemix/inst/doc/Rtreemix.pdf, vignettes/Rtreemix/inst/doc/topologies.pdf vignetteTitles: ClassDiagram.pdf, ExtendedVignette.pdf, Rtreemix, topologies.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Rtreemix/inst/doc/Rtreemix.R Package: RWebServices Version: 1.22.0 Depends: SJava (>= 0.69-4), TypeInfo, methods, tools (>= 2.10.0), R (>= 2.5.0) Imports: RCurl License: file LICENSE Title: Expose R functions as web services through Java/Axis/Apache Description: This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment. biocViews: Infrastructure Author: Nianhua Li, MT Morgan Maintainer: Martin Morgan MD5sum: 01570cf0ef739a43832840f2a5fb8fba source.ver: src/contrib/RWebServices_1.22.0.tar.gz vignettes: vignettes/RWebServices/inst/doc/EnablingPackages.pdf, vignettes/RWebServices/inst/doc/InstallingAndTesting.pdf, vignettes/RWebServices/inst/doc/LessonsLearned.pdf, vignettes/RWebServices/inst/doc/RelatedWork.pdf, vignettes/RWebServices/inst/doc/RToJava.pdf vignetteTitles: Enabling packages as web services, Installing and testing RWebServices and enabled packages, Lessons learned exposing web services, RelatedWork, From R to Java hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/RWebServices/inst/doc/EnablingPackages.R, vignettes/RWebServices/inst/doc/InstallingAndTesting.R, vignettes/RWebServices/inst/doc/LessonsLearned.R, vignettes/RWebServices/inst/doc/RelatedWork.R, vignettes/RWebServices/inst/doc/RToJava.R Package: safe Version: 2.18.0 Depends: R (>= 2.4.0), Biobase, annotate, methods Imports: SparseM, GO.db, annotate, AnnotationDbi, survival, Biobase Suggests: GO.db, GOstats, Rgraphviz, multtest, hu6800.db, survival License: GPL (>= 2) Title: Significance Analysis of Function and Expression Description: SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions. biocViews: GeneExpression, FunctionalAnnotation Author: William T. Barry Maintainer: William T. Barry URL: http://www.duke.edu/~dinbarry/SAFE/ MD5sum: 13dde4e6d832afafe9dc53b7edebad2e source.ver: src/contrib/safe_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/safe_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/safe_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/safe_2.18.0.tgz vignettes: vignettes/safe/inst/doc/SAFEmanual2.pdf vignetteTitles: SAFE manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/safe/inst/doc/SAFEmanual2.R Package: sagenhaft Version: 1.28.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, methods, SparseM, stats, utils License: GPL (>= 2) Title: Collection of functions for reading and comparing SAGE libraries Description: This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts. biocViews: SAGE Author: Tim Beissbarth , with contributions from Gordon Smyth and Lavinia Hyde . Maintainer: Tim Beissbarth URL: http://tagcalling.mbgproject.org MD5sum: 3656eb367968201f9690310ec5f019bb source.ver: src/contrib/sagenhaft_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sagenhaft_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sagenhaft_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sagenhaft_1.28.0.tgz vignettes: vignettes/sagenhaft/inst/doc/SAGEnhaft.pdf vignetteTitles: SAGEnhaft hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sagenhaft/inst/doc/SAGEnhaft.R Package: SAGx Version: 1.32.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase, stats4 Suggests: KEGG.db, hu6800.db, MASS License: GPL-3 Archs: i386, x64 Title: Statistical Analysis of the GeneChip Description: A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed. biocViews: Microarray, OneChannel, Preprocessing, DataImport, Bioinformatics, DifferentialExpression, Clustering, MultipleComparisons Author: Per Broberg Maintainer: Per Broberg, URL: http://home.swipnet.se/pibroberg/expression_hemsida1.html MD5sum: 70cac79f7e14bd2f09169b7c3fb49d59 source.ver: src/contrib/SAGx_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SAGx_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SAGx_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SAGx_1.32.0.tgz vignettes: vignettes/SAGx/inst/doc/samroc-ex.pdf vignetteTitles: samroc - example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SAGx/inst/doc/samroc-ex.R Package: SamSPECTRAL Version: 1.12.0 Depends: R (>= 2.10) Imports: methods License: GPL version 2 or newer Archs: i386, x64 Title: Identifies cell population in flow cytometry data. Description: Given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data sample. For instructions on manual installation, refer to the PDF file provided in the following documentation. biocViews: Bioinformatics, FlowCytometry, CellBiology, Clustering, Cancer, FlowCytData, StemCells, HIV Author: Habil Zare and Parisa Shooshtari Maintainer: Habil Zare MD5sum: 24e444be16fca3a9ebfd4bf8ef5d0f1c source.ver: src/contrib/SamSPECTRAL_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SamSPECTRAL_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SamSPECTRAL_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SamSPECTRAL_1.12.0.tgz vignettes: vignettes/SamSPECTRAL/inst/doc/Clustering_by_SamSPECTRAL.pdf vignetteTitles: A modified spectral clustering method for clustering Flow Cytometry Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SamSPECTRAL/inst/doc/Clustering_by_SamSPECTRAL.R Package: SBMLR Version: 1.54.0 Depends: XML, deSolve License: GPL-2 Title: SBML-R Interface and Analysis Tools Description: This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples. biocViews: GraphsAndNetworks, Pathways, NetworkAnalysis Author: Tomas Radivoyevitch Maintainer: Tomas Radivoyevitch URL: http://epbi-radivot.cwru.edu/SBMLR/SBMLR.html MD5sum: 42c08b85e20ad21e189514a265388d33 source.ver: src/contrib/SBMLR_1.54.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SBMLR_1.54.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SBMLR_1.54.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SBMLR_1.54.0.tgz vignettes: vignettes/SBMLR/inst/doc/BMC.BioInformatics04.pdf, vignettes/SBMLR/inst/doc/manual.pdf, vignettes/SBMLR/inst/doc/quick-start.pdf vignetteTitles: BMC.BioInformatics04.pdf, manual.pdf, Quick intro to SBMLR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SBMLR/inst/doc/quick-start.R Package: SCAN.UPC Version: 1.0.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings Imports: utils, methods Suggests: pd.hg.u95a License: MIT Title: Single-channel array normalization (SCAN) Description: SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. (The Universal Probability of expression Codes (UPC) method is an extension of SCAN and will be added to this package soon.) biocViews: Software, Microarray, Preprocessing Author: Stephen R. Piccolo and W. Evan Johnson Maintainer: Stephen R. Piccolo URL: http://bioconductor.org, http://jlab.bu.edu/software/scan-upc MD5sum: 7671f8c57aafbcf949f707fa4f5aaa90 source.ver: src/contrib/SCAN.UPC_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SCAN.UPC_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SCAN.UPC_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SCAN.UPC_1.0.0.tgz vignettes: vignettes/SCAN.UPC/inst/doc/SCAN.vignette.pdf vignetteTitles: SCAN - Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/SCAN.UPC/inst/doc/SCAN.vignette.R Package: ScISI Version: 1.30.0 Depends: R (>= 2.10), GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable License: LGPL Title: In Silico Interactome Description: Package to create In Silico Interactomes biocViews: GraphsAndNetworks, Proteomics, NetworkInference Author: Tony Chiang Maintainer: Tony Chiang MD5sum: 18bcc4116ef26a48aa3a642441e02b82 source.ver: src/contrib/ScISI_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ScISI_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ScISI_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ScISI_1.30.0.tgz vignettes: vignettes/ScISI/inst/doc/vignette.pdf vignetteTitles: ScISI Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ScISI/inst/doc/vignette.R dependsOnMe: PCpheno, ppiStats, SLGI importsMe: PCpheno, SLGI suggestsMe: RpsiXML Package: segmentSeq Version: 1.10.1 Depends: R (>= 2.3.0), methods, baySeq (>= 1.11.1), ShortRead, GenomicRanges, IRanges Imports: baySeq, graphics, grDevices, IRanges, methods, utils, GenomicRanges Suggests: snow License: GPL-3 Title: Methods for identifying small RNA loci from high-throughput sequencing data Description: High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery. biocViews: Bioinformatics, HighThroughputSequencing, MultipleComparisons Author: Thomas J. Hardcastle Maintainer: Thomas J. Hardcastle MD5sum: 3e47e7afbdd8f9b63233c67cc9aa479d source.ver: src/contrib/segmentSeq_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/segmentSeq_1.10.1.zip win64.binary.ver: bin/windows64/contrib/2.15/segmentSeq_1.10.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/segmentSeq_1.10.1.tgz vignettes: vignettes/segmentSeq/inst/doc/segmentSeq.pdf vignetteTitles: segmentSeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/segmentSeq/inst/doc/segmentSeq.R Package: seqbias Version: 1.6.0 Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods Imports: zlibbioc LinkingTo: Rsamtools Suggests: Rsamtools, ggplot2 License: LGPL-3 Archs: i386, x64 Title: Estimation of per-position bias in high-throughput sequencing data Description: This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence. biocViews: Sequencing, HighThroughputSequencing Author: Daniel Jones Maintainer: Daniel Jones MD5sum: 769295cc544d5545bc8b1518011bbff4 source.ver: src/contrib/seqbias_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/seqbias_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/seqbias_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/seqbias_1.6.0.tgz vignettes: vignettes/seqbias/inst/doc/overview.pdf vignetteTitles: Assessing and Adjusting for Technical Bias in High Throughput Sequencing Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seqbias/inst/doc/overview.R dependsOnMe: ReQON Package: seqLogo Version: 1.24.0 Depends: methods, grid License: LGPL (>= 2) Title: Sequence logos for DNA sequence alignments Description: seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990). biocViews: SequenceMatching Author: Oliver Bembom Maintainer: Oliver Bembom MD5sum: 26d8427faeb909346d2fa4f32f6d3ebf source.ver: src/contrib/seqLogo_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/seqLogo_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/seqLogo_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/seqLogo_1.24.0.tgz vignettes: vignettes/seqLogo/inst/doc/seqLogo.pdf vignetteTitles: Sequence logos for DNA sequence alignments hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seqLogo/inst/doc/seqLogo.R dependsOnMe: rGADEM importsMe: motifRG, PWMEnrich, rGADEM suggestsMe: BCRANK, MotifDb Package: ShortRead Version: 1.16.4 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.4), GenomicRanges (>= 1.7.43), Biostrings (>= 2.25.6), lattice, Rsamtools (>= 1.7.42), latticeExtra Imports: BiocGenerics, IRanges, GenomicRanges, Biostrings, Biobase, hwriter, Rsamtools, zlibbioc, lattice LinkingTo: IRanges, Biostrings Suggests: biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi Enhances: Rmpi, parallel License: Artistic-2.0 Archs: i386, x64 Title: Classes and methods for high-throughput short-read sequencing data. Description: Base classes, functions, and methods for representation of high-throughput, short-read sequencing data. biocViews: DataImport, Sequencing, HighThroughputSequencing, QualityControl Author: Martin Morgan, Michael Lawrence, Simon Anders Maintainer: Bioconductor Package Maintainer MD5sum: d93c39673d98d300592e07265ce3d862 source.ver: src/contrib/ShortRead_1.16.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/ShortRead_1.16.4.zip win64.binary.ver: bin/windows64/contrib/2.15/ShortRead_1.16.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ShortRead_1.16.4.tgz vignettes: vignettes/ShortRead/inst/doc/Overview.pdf, vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf vignetteTitles: An introduction to ShortRead, ShortRead_and_HilbertVis.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ShortRead/inst/doc/Overview.R dependsOnMe: chipseq, ChIPseqR, easyRNASeq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, segmentSeq importsMe: ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, HiTC, nucleR, OTUbase, R453Plus1Toolbox, Rolexa, rSFFreader suggestsMe: CSAR, DBChIP, Genominator, PICS, PING, R453Plus1Toolbox, Repitools, Rsamtools Package: sigaR Version: 1.2.1 Depends: Biobase, CGHbase, methods, mvtnorm, penalized Imports: corpcor (>= 1.6.2), graphics, igraph, marray, MASS, mvtnorm, quadprog, penalized (>= 0.9-39), snowfall, stats License: GPL (>= 2) Title: statistics for integrative genomics analyses in R Description: Facilites the joint analysis of high-throughput data from multiple molecular levels. Contains functions for manipulation of objects, various analysis types, and some visualization. biocViews: Microarray, Bioinformatics, DifferentialExpression, aCGH, GeneExpression, Pathways Author: Wessel N. van Wieringen Maintainer: Wessel N. van Wieringen URL: http://www.few.vu.nl/~wvanwie MD5sum: 92c073b8d0b2f647c1317633e91566e0 source.ver: src/contrib/sigaR_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/sigaR_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/sigaR_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sigaR_1.2.1.tgz vignettes: vignettes/sigaR/inst/doc/sigaR.pdf, vignettes/sigaR/inst/doc/statisticalUnit.pdf vignetteTitles: sigaR, statisticalUnit.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sigaR/inst/doc/sigaR.R Package: siggenes Version: 1.32.0 Depends: methods, Biobase, multtest, splines, graphics Imports: stats4 Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5) License: LGPL (>= 2) Title: Multiple testing using SAM and Efron's empirical Bayes approaches Description: Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM). biocViews: MultipleComparisons, Microarray, GeneExpression, SNP, ExonArray, DifferentialExpression Author: Holger Schwender Maintainer: Holger Schwender MD5sum: 772d7f8ca1f47a921ef099111359e5f5 source.ver: src/contrib/siggenes_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/siggenes_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/siggenes_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/siggenes_1.32.0.tgz vignettes: vignettes/siggenes/inst/doc/siggenes.pdf, vignettes/siggenes/inst/doc/siggenesRnews.pdf vignetteTitles: siggenes Manual, siggenesRnews.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/siggenes/inst/doc/siggenes.R htmlDocs: vignettes/siggenes/inst/doc/identify.sam.html, vignettes/siggenes/inst/doc/plot.ebam.html, vignettes/siggenes/inst/doc/plot.finda0.html, vignettes/siggenes/inst/doc/plot.sam.html, vignettes/siggenes/inst/doc/print.ebam.html, vignettes/siggenes/inst/doc/print.finda0.html, vignettes/siggenes/inst/doc/print.sam.html, vignettes/siggenes/inst/doc/summary.ebam.html, vignettes/siggenes/inst/doc/summary.sam.html dependsOnMe: KCsmart, oneChannelGUI importsMe: charm, GeneSelector, minfi suggestsMe: GeneSelector, logicFS, XDE Package: sigPathway Version: 1.26.0 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 Archs: i386, x64 Title: Pathway Analysis Description: Conducts pathway analysis by calculating the NT_k and NE_k statistics as described in Tian et al. (2005) biocViews: Bioinformatics, DifferentialExpression, MultipleComparisons Author: Weil Lai (optimized R and C code), Lu Tian and Peter Park (algorithm development and initial R code) Maintainer: Weil Lai URL: http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102, http://www.chip.org/~ppark/Supplements/PNAS05.html MD5sum: 5ddb41201f942faf8041912e5d4ef6ae source.ver: src/contrib/sigPathway_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sigPathway_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sigPathway_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sigPathway_1.26.0.tgz vignettes: vignettes/sigPathway/inst/doc/sigPathway-vignette.pdf vignetteTitles: sigPathway hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sigPathway/inst/doc/sigPathway-vignette.R Package: SIM Version: 1.28.2 Depends: R (>= 2.4), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) Archs: i386, x64 Title: Integrated Analysis on two human genomic datasets Description: Finds associations between two human genomic datasets. biocViews: Microarray, Bioinformatics, Visualization Author: Renee X. de Menezes and Judith M. Boer Maintainer: Renee X. de Menezes MD5sum: c8cc9d5e8ee70af1805bf0be41379bb1 source.ver: src/contrib/SIM_1.28.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/SIM_1.28.2.zip win64.binary.ver: bin/windows64/contrib/2.15/SIM_1.28.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SIM_1.28.2.tgz vignettes: vignettes/SIM/inst/doc/SIM.pdf vignetteTitles: SIM vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SIM/inst/doc/SIM.R Package: simpleaffy Version: 2.34.0 Depends: R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6), genefilter, gcrma Imports: methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma License: GPL (>= 2) Archs: i386, x64 Title: Very simple high level analysis of Affymetrix data Description: Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures... biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Transcription, DataImport, Bioinformatics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Crispin J Miller Maintainer: Crispin Miller URL: http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/ MD5sum: 63e0aa6b2b1737ee748cd55f646a8e80 source.ver: src/contrib/simpleaffy_2.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/simpleaffy_2.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/simpleaffy_2.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/simpleaffy_2.34.0.tgz vignettes: vignettes/simpleaffy/inst/doc/QCandSimpleaffy.pdf, vignettes/simpleaffy/inst/doc/simpleAffy.pdf vignetteTitles: QCandSimpleaffy.pdf, simpleaffy primer hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/simpleaffy/inst/doc/simpleAffy.R dependsOnMe: yaqcaffy importsMe: affyQCReport, arrayMvout, arrayQualityMetrics suggestsMe: AffyExpress, ArrayTools Package: sizepower Version: 1.28.0 Depends: stats License: LGPL Title: Sample Size and Power Calculation in Micorarray Studies Description: This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice. biocViews: Microarray, Bioinformatics Author: Weiliang Qiu and Mei-Ling Ting Lee and George Alex Whitmore Maintainer: Weiliang Qiu MD5sum: 6183136e05416d96c922f8a277578702 source.ver: src/contrib/sizepower_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sizepower_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sizepower_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sizepower_1.28.0.tgz vignettes: vignettes/sizepower/inst/doc/sizepower.pdf vignetteTitles: package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sizepower/inst/doc/sizepower.R suggestsMe: oneChannelGUI Package: SJava Version: 0.84.0 Depends: R (>= 2.10.0), methods Imports: methods License: GPL (>= 2) Title: The Omegahat interface for R and Java. Description: An interface from R to Java to create and call Java objects and methods. biocViews: Infrastructure Author: Duncan Temple Lang, John Chambers Maintainer: Martin Morgan MD5sum: 0366ad5aad8934bb0b19a23a5fdb08fe source.ver: src/contrib/SJava_0.84.0.tar.gz hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: RWebServices Package: SLGI Version: 1.18.0 Depends: R (>= 2.10), ScISI, lattice Imports: AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice, methods, stats, BiocGenerics Suggests: GO.db, org.Sc.sgd.db License: Artistic-2.0 Title: Synthetic Lethal Genetic Interaction Description: A variety of data files and functions for the analysis of genetic interactions biocViews: GraphsAndNetworks, Proteomics, Genetics, NetworkAnalysis Author: Nolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and Robert Gentleman Maintainer: Nolwenn Le Meur MD5sum: 009af5b9c44567313c8d5bbd2e833ebe source.ver: src/contrib/SLGI_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SLGI_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SLGI_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SLGI_1.18.0.tgz vignettes: vignettes/SLGI/inst/doc/SLGI.pdf vignetteTitles: SLGI Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SLGI/inst/doc/SLGI.R dependsOnMe: PCpheno Package: SLqPCR Version: 1.24.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) Title: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH Description: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH biocViews: Bioinformatics, MicrotitrePlateAssay, qPCR Author: Matthias Kohl Maintainer: Matthias Kohl MD5sum: b016ecb2c15d8bb854625eff90d3e46b source.ver: src/contrib/SLqPCR_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SLqPCR_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SLqPCR_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SLqPCR_1.24.0.tgz vignettes: vignettes/SLqPCR/inst/doc/SLqPCR.pdf vignetteTitles: SLqPCR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SLqPCR/inst/doc/SLqPCR.R suggestsMe: EasyqpcR Package: SMAP Version: 1.22.0 Depends: R (>= 2.10), methods License: GPL-2 Archs: i386, x64 Title: A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling Description: Functions and classes for DNA copy number profiling of array-CGH data biocViews: Microarray, TwoChannel, CopyNumberVariants Author: Robin Andersson Maintainer: Robin Andersson MD5sum: a19af9b7b46891c3c758c9c0b0b13112 source.ver: src/contrib/SMAP_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SMAP_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SMAP_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SMAP_1.22.0.tgz vignettes: vignettes/SMAP/inst/doc/SMAP.pdf vignetteTitles: SMAP hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SMAP/inst/doc/SMAP.R Package: snapCGH Version: 1.28.0 Depends: limma, DNAcopy, methods Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils License: GPL Archs: i386, x64 Title: Segmentation, normalisation and processing of aCGH data. Description: Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. biocViews: Microarray, CopyNumberVariants, TwoChannel, Preprocessing Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas Hardcastle, Natalie P. Thorne Maintainer: John Marioni MD5sum: db4c2a1b1bd2721750137d86b25f204a source.ver: src/contrib/snapCGH_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/snapCGH_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/snapCGH_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/snapCGH_1.28.0.tgz vignettes: vignettes/snapCGH/inst/doc/snapCGHguide.pdf vignetteTitles: Segmentation Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/snapCGH/inst/doc/snapCGHguide.R dependsOnMe: ADaCGH2 suggestsMe: beadarraySNP Package: snm Version: 1.6.0 Depends: R(>= 2.12.0), lme4, splines, corpcor License: LGPL Title: Supervised Normalization of Microarrays Description: SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest. biocViews: Microarray, OneChannel, TwoChannel, MultiChannel, DifferentialExpression, ExonArray, GeneExpression, Transcription, MultipleComparisons, Preprocessing, QualityControl Author: Brig Mecham and John D. Storey Maintainer: Brig Mecham MD5sum: 277cab311d5e0d86f0c8ec034327954e source.ver: src/contrib/snm_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/snm_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/snm_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/snm_1.6.0.tgz vignettes: vignettes/snm/inst/doc/snm.pdf vignetteTitles: snm Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/snm/inst/doc/snm.R Package: SNPchip Version: 2.4.0 Depends: R (>= 2.14.0) Imports: graphics, lattice, grid, foreach, utils, methods, oligoClasses (>= 1.19.30), Biobase, GenomicRanges Suggests: crlmm, IRanges, RUnit Enhances: doSNOW, VanillaICE, RColorBrewer License: LGPL (>= 2) Title: Visualizations for copy number alterations Description: This package defines methods for visualizing high-throughput genomic data biocViews: CopyNumberVariants, SNP, GeneticVariability, Visualization Author: Robert Scharpf and Ingo Ruczinski Maintainer: Robert Scharpf URL: http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html MD5sum: 0df8101997bcd6910feaec30a3eb539b source.ver: src/contrib/SNPchip_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SNPchip_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SNPchip_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SNPchip_2.4.0.tgz vignettes: vignettes/SNPchip/inst/doc/PlottingIdiograms.pdf vignetteTitles: Plotting Idiograms hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SNPchip/inst/doc/PlottingIdiograms.R dependsOnMe: mBPCR importsMe: crlmm, MinimumDistance, phenoTest suggestsMe: Category, oligoClasses, VanillaICE Package: snpStats Version: 1.8.2 Depends: R(>= 2.10.0), survival, methods, Matrix Imports: graphics, grDevices, methods, stats, survival, utils, Matrix, BiocGenerics Suggests: hexbin License: GPL-3 Archs: i386, x64 Title: SnpMatrix and XSnpMatrix classes and methods Description: Classes and statistical methods for large SNP association studies, extending the snpMatrix package (now removed) biocViews: Microarray, SNP, GeneticVariability Author: David Clayton Maintainer: David Clayton MD5sum: 1b909fd6f7152b9e91d299b7413afd74 source.ver: src/contrib/snpStats_1.8.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/snpStats_1.8.2.zip win64.binary.ver: bin/windows64/contrib/2.15/snpStats_1.8.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/snpStats_1.8.2.tgz vignettes: vignettes/snpStats/inst/doc/data-input-vignette.pdf, vignettes/snpStats/inst/doc/differences.pdf, vignettes/snpStats/inst/doc/imputation-vignette.pdf, vignettes/snpStats/inst/doc/ld-vignette.pdf, vignettes/snpStats/inst/doc/pca-vignette.pdf, vignettes/snpStats/inst/doc/snpStats-vignette.pdf, vignettes/snpStats/inst/doc/tdt-vignette.pdf vignetteTitles: Data input, snpMatrix-differences, Imputation and meta-analysis, LD statistics, Principal components analysis, snpStats introduction, TDT tests hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/snpStats/inst/doc/data-input-vignette.R, vignettes/snpStats/inst/doc/differences.R, vignettes/snpStats/inst/doc/imputation-vignette.R, vignettes/snpStats/inst/doc/ld-vignette.R, vignettes/snpStats/inst/doc/pca-vignette.R, vignettes/snpStats/inst/doc/snpStats-vignette.R, vignettes/snpStats/inst/doc/tdt-vignette.R htmlDocs: vignettes/snpStats/inst/doc/index.html dependsOnMe: GGBase, gwascat importsMe: FunciSNP, GGtools suggestsMe: crlmm, GWASTools, VariantAnnotation Package: spade Version: 1.6.0 Depends: R (>= 2.11), igraph0 Imports: Biobase, flowCore Suggests: flowViz License: GPL-2 Archs: i386, x64 Title: SPADE -- An analysis and visualization tool for Flow Cytometry Description: SPADE, or Spanning tree Progression of Density normalized Events, is an analysis and visualization tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes. biocViews: FlowCytometry, GraphsAndNetworks, GUI, Visualization, Clustering Author: M. Linderman, P. Qiu, E. Simonds, Z. Bjornson Maintainer: Michael Linderman URL: http://cytospade.org MD5sum: 4590a0d20855e5a63efe93b27e9cc056 source.ver: src/contrib/spade_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/spade_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/spade_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spade_1.6.0.tgz vignettes: vignettes/spade/inst/doc/SPADE.pdf vignetteTitles: spade package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/spade/inst/doc/SPADE.R Package: SpeCond Version: 1.12.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>=2) Title: Condition specific detection from expression data Description: This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression. biocViews: Microarray, DifferentialExpression, Bioinformatics, MultipleComparisons, Clustering, ReportWriting Author: Florence Cavalli Maintainer: Florence Cavalli MD5sum: af49b00b65ae0d92b268af5b6da65625 source.ver: src/contrib/SpeCond_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SpeCond_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SpeCond_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SpeCond_1.12.0.tgz vignettes: vignettes/SpeCond/inst/doc/SpeCond.pdf vignetteTitles: SpeCond hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SpeCond/inst/doc/SpeCond.R Package: SPIA Version: 2.8.0 Depends: R (>= 2.10), graphics Imports: graphics Suggests: graph, Rgraphviz, KEGGgraph, hgu133plus2.db License: GPL (>= 2) Title: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations Description: This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study. biocViews: Microarray, GraphsAndNetworks, NetworkEnrichment, Pathways Author: Adi Laurentiu Tarca , Purvesh Kathri and Sorin Draghici Maintainer: Adi Laurentiu Tarca URL: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1 MD5sum: 7ad7fa734ff24aa6de6d4bca112a4cfd source.ver: src/contrib/SPIA_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SPIA_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SPIA_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SPIA_2.8.0.tgz vignettes: vignettes/SPIA/inst/doc/SPIA.pdf vignetteTitles: SPIA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SPIA/inst/doc/SPIA.R suggestsMe: graphite, KEGGgraph Package: spikeLI Version: 2.18.0 Imports: graphics, grDevices, stats, utils License: GPL-2 Title: Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool Description: SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006). biocViews: Microarray, QualityControl Author: Delphine Baillon, Paul Leclercq , Sarah Ternisien, Thomas Heim, Enrico Carlon Maintainer: Enrico Carlon MD5sum: be40bcbb40fc4b22cc2bb472ec8927cf source.ver: src/contrib/spikeLI_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/spikeLI_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/spikeLI_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spikeLI_2.18.0.tgz vignettes: vignettes/spikeLI/inst/doc/collapse_A14.pdf, vignettes/spikeLI/inst/doc/Ivsc.pdf, vignettes/spikeLI/inst/doc/IvsDG_TagE.pdf, vignettes/spikeLI/inst/doc/langmuir2.pdf, vignettes/spikeLI/inst/doc/spikeLI.pdf vignetteTitles: collapse_A14.pdf, Ivsc.pdf, IvsDG_TagE.pdf, langmuir2.pdf, spikeLI hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spikeLI/inst/doc/spikeLI.R Package: spkTools Version: 1.14.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) Title: Methods for Spike-in Arrays Description: The package contains functions that can be used to compare expression measures on different array platforms. biocViews: Software, AssayTechnologies, Microarray Author: Matthew N McCall , Rafael A Irizarry Maintainer: Matthew N McCall URL: http://bioconductor.org MD5sum: 17425728178716e0bb23cbe61fb895da source.ver: src/contrib/spkTools_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/spkTools_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/spkTools_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spkTools_1.14.0.tgz vignettes: vignettes/spkTools/inst/doc/spkDoc.pdf vignetteTitles: spkTools: Spike-in Data Analysis and Visualization hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spkTools/inst/doc/spkDoc.R Package: splicegear Version: 1.30.0 Depends: R (>= 2.6.0), methods, Biobase(>= 2.5.5) Imports: annotate, Biobase, graphics, grDevices, grid, methods, utils, XML License: LGPL Title: splicegear Description: A set of tools to work with alternative splicing biocViews: Infrastructure, Transcription Author: Laurent Gautier Maintainer: Laurent Gautier MD5sum: 7813c754b2d7d47f296b066024dadc07 source.ver: src/contrib/splicegear_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/splicegear_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/splicegear_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/splicegear_1.30.0.tgz vignettes: vignettes/splicegear/inst/doc/splicegear.pdf vignetteTitles: splicegear Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/splicegear/inst/doc/splicegear.R Package: splots Version: 1.24.0 Imports: grid, RColorBrewer License: LGPL Title: Visualization of high-throughput assays in microtitre plate or slide format Description: The splots package provides the plotScreen function for visualising data in microtitre plate or slide format. biocViews: Visualization, HighThroughputSequencing, MicrotitrePlateAssay Author: Wolfgang Huber, Oleg Sklyar Maintainer: Wolfgang Huber MD5sum: f2dcac542e11df5aad97284c75a907e6 source.ver: src/contrib/splots_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/splots_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/splots_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/splots_1.24.0.tgz vignettes: vignettes/splots/inst/doc/splotsHOWTO.pdf vignetteTitles: Visualization of data from assays in microtitre plate or slide format hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/splots/inst/doc/splotsHOWTO.R dependsOnMe: cellHTS2 importsMe: RNAinteract, RNAither Package: spotSegmentation Version: 1.32.0 Depends: R (>= 2.10), mclust License: GPL (>= 2) Title: Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots Description: Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington. biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Qunhua Li, Chris Fraley, Adrian Raftery Department of Statistics, University of Washington Maintainer: Chris Fraley URL: http://www.stat.washington.edu/fraley MD5sum: 74084cce372d13c76954fe138afc8a82 source.ver: src/contrib/spotSegmentation_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/spotSegmentation_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/spotSegmentation_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spotSegmentation_1.32.0.tgz vignettes: vignettes/spotSegmentation/inst/doc/spotsegdoc.pdf vignetteTitles: spotsegdoc.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SQUADD Version: 1.8.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>=2) Title: Add-on of the SQUAD Software Description: This package SQUADD is a SQUAD add-on. It permits to generate SQUAD simulation matrix, prediction Heat-Map and Correlation Circle from PCA analysis. biocViews: GraphsAndNetworks, NetworkAnalysis, Visualization Author: Martial Sankar, supervised by Christian Hardtke and Ioannis Xenarios Maintainer: Martial Sankar URL: http://www.unil.ch/dbmv/page21142_en.html MD5sum: 009e89b8344454621b948fb1855bf73b source.ver: src/contrib/SQUADD_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SQUADD_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SQUADD_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SQUADD_1.8.0.tgz vignettes: vignettes/SQUADD/inst/doc/SQUADD_ERK.pdf, vignettes/SQUADD/inst/doc/SQUADD.pdf vignetteTitles: SQUADD package, SQUADD package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SQUADD/inst/doc/SQUADD_ERK.R, vignettes/SQUADD/inst/doc/SQUADD.R Package: SRAdb Version: 1.12.1 Depends: RSQLite (>= 0.8-4) , graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 Title: A compilation of metadata from NCBI SRA and tools Description: The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. sra or sra-lite files can be downloaded for doing alignment locally. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata. biocViews: Infrastructure, HighThroughputSequencing, DataImport Author: Jack Zhu and Sean Davis Maintainer: Jack Zhu URL: http://watson.nci.nih.gov/ MD5sum: 076795002b530b63997d26d166d5bbc5 source.ver: src/contrib/SRAdb_1.12.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/SRAdb_1.12.1.zip win64.binary.ver: bin/windows64/contrib/2.15/SRAdb_1.12.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SRAdb_1.12.1.tgz vignettes: vignettes/SRAdb/inst/doc/SRAdb.pdf vignetteTitles: Using SRAdb to Query the Sequence Read Archive hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SRAdb/inst/doc/SRAdb.R Package: sscore Version: 1.30.0 Depends: R (>= 1.8.0), affy, affyio Suggests: affydata License: GPL (>= 2) Title: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays Description: This package contains an implementation of the S-Score algorithm as described by Zhang et al (2002). biocViews: Bioinformatics, DifferentialExpression Author: Richard Kennedy , based on C++ code from Li Zhang and Borland Delphi code from Robnet Kerns . Maintainer: Richard Kennedy URL: http://home.att.net/~richard-kennedy/professional.html MD5sum: a6fa5f616d030173a3aa06957960d506 source.ver: src/contrib/sscore_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sscore_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sscore_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sscore_1.30.0.tgz vignettes: vignettes/sscore/inst/doc/sscore.pdf vignetteTitles: SScore primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sscore/inst/doc/sscore.R Package: ssize Version: 1.32.0 Depends: gdata, xtable License: LGPL Title: Estimate Microarray Sample Size Description: Functions for computing and displaying sample size information for gene expression arrays. biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Gregory R. Warnes, Peng Liu, and Fasheng Li Maintainer: Gregory R. Warnes MD5sum: be2534d4ac3e0a31cd0376ba0399872e source.ver: src/contrib/ssize_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ssize_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ssize_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ssize_1.32.0.tgz vignettes: vignettes/ssize/inst/doc/ssize.pdf vignetteTitles: package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ssize/inst/doc/ssize.R suggestsMe: oneChannelGUI Package: SSPA Version: 1.14.2 Depends: R (>= 2.8), methods, qvalue Imports: graphics, limma, methods, stats Suggests: multtest, quadprog, splines License: GPL (>= 2) Archs: i386, x64 Title: Sample Size and Power Analysis for Microarray Data Description: Sample size and power analysis for microarray data, where two groups are analysed. biocViews: Microarray Author: Maarten van Iterson Maintainer: Maarten van Iterson URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html MD5sum: 789e53356ff034472ed0d85f877cdecb source.ver: src/contrib/SSPA_1.14.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/SSPA_1.14.2.zip win64.binary.ver: bin/windows64/contrib/2.15/SSPA_1.14.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SSPA_1.14.2.tgz vignettes: vignettes/SSPA/inst/doc/figChunk17.pdf, vignettes/SSPA/inst/doc/SSPA.pdf vignetteTitles: figChunk17.pdf, SSPA vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SSPA/inst/doc/SSPA.R Package: staRank Version: 1.0.0 Depends: methods, cellHTS2, R (>= 2.10) License: GPL Title: Stability Ranking Description: Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling. biocViews: Bioinformatics, MultipleComparisons, CellBiology, CellBasedAssays, MicrotitrePlateAssay Author: Juliane Siebourg, Niko Beerenwinkel Maintainer: Juliane Siebourg MD5sum: b5dd0738c9cca0c69faec77a742cd1e9 source.ver: src/contrib/staRank_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/staRank_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/staRank_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/staRank_1.0.0.tgz vignettes: vignettes/staRank/inst/doc/staRank.pdf vignetteTitles: Using staRank hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/staRank/inst/doc/staRank.R Package: Starr Version: 1.14.1 Depends: Ringo, affy, affxparser Imports: pspline, MASS, zlibbioc License: Artistic-2.0 Archs: i386, x64 Title: Simple tiling array analysis of Affymetrix ChIP-chip data Description: Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome. biocViews: Microarray,OneChannel,DataImport,QualityControl,Preprocessing,ChIPchip Author: Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch Maintainer: Benedikt Zacher MD5sum: 9d9a366de1b960f52aa6cefafb520879 source.ver: src/contrib/Starr_1.14.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/Starr_1.14.1.zip win64.binary.ver: bin/windows64/contrib/2.15/Starr_1.14.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Starr_1.14.1.tgz vignettes: vignettes/Starr/inst/doc/Starr.pdf vignetteTitles: Simple tiling array analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Starr/inst/doc/Starr.R Package: stepNorm Version: 1.30.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL Title: Stepwise normalization functions for cDNA microarrays Description: Stepwise normalization functions for cDNA microarray data. biocViews: Microarray, TwoChannel, Preprocessing Author: Yuanyuan Xiao , Yee Hwa (Jean) Yang Maintainer: Yuanyuan Xiao URL: http://www.biostat.ucsf.edu/jean/ MD5sum: ce38bffafdba0905cdfa187499971b32 source.ver: src/contrib/stepNorm_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/stepNorm_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/stepNorm_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/stepNorm_1.30.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stepwiseCM Version: 1.4.0 Depends: R (>= 2.14), randomForest, MAclinical, tspair, pamr, snowfall, glmpath, penalized, e1071 License: GPL (http://www.gnu.org/copyleft/gpl.html) Title: Stepwise Classification of Cancer Samples using Clinical and Molecular Data Description: Stepwise classification of cancer samples using both clinical and molecular data Author: Askar Obulkasim Maintainer: Askar Obulkasim MD5sum: 7f0a816b36a1c51021faf92011dc68c5 source.ver: src/contrib/stepwiseCM_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/stepwiseCM_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/stepwiseCM_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/stepwiseCM_1.4.0.tgz vignettes: vignettes/stepwiseCM/inst/doc/stepwiseCM.pdf vignetteTitles: stepwiseCM hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/stepwiseCM/inst/doc/stepwiseCM.R Package: Streamer Version: 1.4.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), Rgraphviz License: Artistic-2.0 Archs: i386, x64 Title: Enabling stream processing of large files Description: Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is 'streamed' from disk into R via a `producer' and through a series of `consumers' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details. biocViews: Infrastructure, DataImport Author: Martin Morgan, Nishant Gopalakrishnan Maintainer: Martin Morgan MD5sum: fe83281f8f6d3cbec30bdfdf7d41dc31 source.ver: src/contrib/Streamer_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Streamer_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Streamer_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Streamer_1.4.0.tgz vignettes: vignettes/Streamer/inst/doc/Streamer.pdf vignetteTitles: Streamer: A simple example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Streamer/inst/doc/Streamer.R Package: survcomp Version: 1.8.1 Depends: R (>= 2.10), survival, prodlim Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta Suggests: Hmisc, CPE, clinfun, survJamda, Biobase, xtable License: Artistic-2.0 Archs: i386, x64 Title: Performance Assessment and Comparison for Survival Analysis Description: R package providing functions to assess and to compare the performance of risk prediction (survival) models. biocViews: GeneExpression, DifferentialExpression, Visualization Author: Benjamin Haibe-Kains, Markus Schroeder, Catharina Olsen, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen URL: http://compbio.dfci.harvard.edu MD5sum: 6d3a8115723d946788e31eb19087453e source.ver: src/contrib/survcomp_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/survcomp_1.8.1.zip win64.binary.ver: bin/windows64/contrib/2.15/survcomp_1.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/survcomp_1.8.1.tgz vignettes: vignettes/survcomp/inst/doc/survcomp.pdf vignetteTitles: SurvComp: a package for performance assessment and comparison for survival analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/survcomp/inst/doc/survcomp.R dependsOnMe: genefu Package: sva Version: 3.4.0 Depends: R (>= 2.8), corpcor, mgcv Imports: graphics, stats Suggests: limma,pamr,bladderbatch License: Artistic-2.0 Archs: i386, x64 Title: Surrogate Variable Analysis Description: The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in two ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS) and (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics). Surrogate variable analysis and ComBat were developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved. biocViews: Microarray,Statistics,Preprocessing,MultipleComparisons Author: Jeffrey T. Leek , W. Evan Johnson , Hilary S. Parker , Andrew E. Jaffe , John D. Storey , Maintainer: Jeffrey T. Leek MD5sum: 249351a29adcd17008828218188189cc source.ver: src/contrib/sva_3.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sva_3.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sva_3.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sva_3.4.0.tgz vignettes: vignettes/sva/inst/doc/sva.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sva/inst/doc/sva.R importsMe: trigger Package: synapter Version: 1.0.1 Depends: R (>= 2.15), methods, MSnbase Imports: hwriter, tcltk, tcltk2, RColorBrewer, lattice, qvalue, multtest, utils, Biobase Suggests: synapterdata, knitr, xtable License: GPL-2 Title: Label-free data analysis pipeline for optimal identification and quantitation Description: The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy. biocViews: Bioinformatics, MassSpectrometry, Proteomics, GUI Author: Laurent Gatto, Pavel V. Shliaha and Nick J. Bond Maintainer: Laurent Gatto URL: http://lgatto.github.com/synapter/ MD5sum: 0befe93da2bcfc7e17323b9f5bfe4581 source.ver: src/contrib/synapter_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/synapter_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/synapter_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/synapter_1.0.1.tgz vignettes: vignettes/synapter/inst/doc/synapter.pdf vignetteTitles: synapter hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/synapter/inst/doc/synapter.R Package: TargetSearch Version: 1.14.1 Depends: R (>= 2.7.0), mzR, methods Imports: graphics, grDevices, methods, stats, tcltk, utils Suggests: TargetSearchData License: GPL (>= 2) Archs: i386, x64 Title: A package for the analysis of GC-MS metabolite profiling data. Description: This packages provides a targeted pre-processing method for GC-MS data. biocViews: MassSpectrometry,Preprocessing Author: Alvaro Cuadros-Inostroza , Jan Lisec , Henning Redestig , Matt Hannah Maintainer: Alvaro Cuadros-Inostroza MD5sum: a3b57ae617d448aefb6445242c213e7d source.ver: src/contrib/TargetSearch_1.14.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/TargetSearch_1.14.1.zip win64.binary.ver: bin/windows64/contrib/2.15/TargetSearch_1.14.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TargetSearch_1.14.1.tgz vignettes: vignettes/TargetSearch/inst/doc/RICorrection.pdf, vignettes/TargetSearch/inst/doc/TargetSearch.pdf vignetteTitles: RI correction, The TargetSearch Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TargetSearch/inst/doc/RICorrection.R, vignettes/TargetSearch/inst/doc/TargetSearch.R Package: TDARACNE Version: 1.8.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 Title: Network reverse engineering from time course data. Description: To infer gene networks from time-series measurements is a current challenge into bioinformatics research area. In order to detect dependencies between genes at different time delays, we propose an approach to infer gene regulatory networks from time-series measurements starting from a well known algorithm based on information theory. The proposed algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. biocViews: Microarray, TimeCourse Author: Zoppoli P.,Morganella S., Ceccarelli M. Maintainer: Zoppoli Pietro MD5sum: a8fa6de3889e57e1ee90a38c36dff0fc source.ver: src/contrib/TDARACNE_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TDARACNE_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TDARACNE_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TDARACNE_1.8.0.tgz vignettes: vignettes/TDARACNE/inst/doc/TDARACNE.pdf vignetteTitles: TDARACNE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TDARACNE/inst/doc/TDARACNE.R Package: TEQC Version: 2.6.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) Title: Quality control for target capture experiments Description: Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on. biocViews: QualityControl, Microarray, HighThroughputSequencing, Bioinformatics, Genetics Author: M. Hummel, S. Bonnin, E. Lowy, G. Roma Maintainer: Manuela Hummel MD5sum: a539311e2924979de6ac5364ef256471 source.ver: src/contrib/TEQC_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TEQC_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TEQC_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TEQC_2.6.0.tgz vignettes: vignettes/TEQC/inst/doc/TEQC.pdf vignetteTitles: TEQC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TEQC/inst/doc/TEQC.R Package: ternarynet Version: 1.2.0 Depends: R (>= 2.10.0), methods Imports: utils, igraph License: GPL (>= 2) Archs: i386, x64 Title: Ternary Network Estimation Description: A computational Bayesian approach to ternary gene regulatory network estimation from gene perturbation experiments. biocViews: Software, CellBiology, GraphsAndNetworks, Bioinformatics Author: Matthew N. McCall , Anthony Almudevar Maintainer: Matthew N. McCall MD5sum: 0c80e63acc33091ff275b69c58fdb988 source.ver: src/contrib/ternarynet_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ternarynet_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ternarynet_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ternarynet_1.2.0.tgz vignettes: vignettes/ternarynet/inst/doc/ternarynet.pdf vignetteTitles: ternarynet: A Computational Bayesian Approach to Ternary Network Estimation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ternarynet/inst/doc/ternarynet.R Package: tigre Version: 1.12.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, BiocGenerics, Biobase, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite Suggests: puma, drosgenome1.db, annotate, lumi License: AGPL-3 Archs: i386, x64 Title: Transcription factor Inference through Gaussian process Reconstruction of Expression Description: The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF. biocViews: Microarray, Bioinformatics, TimeCourse, GeneExpression, Transcription Author: Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence Maintainer: Antti Honkela URL: http://www.bioinf.manchester.ac.uk/resources/tiger/ MD5sum: 55e4daacdecd439123d96fdef95b47ec source.ver: src/contrib/tigre_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/tigre_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/tigre_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tigre_1.12.0.tgz vignettes: vignettes/tigre/inst/doc/tigre.pdf, vignettes/tigre/inst/doc/tigre_quick.pdf vignetteTitles: tigre User Guide, tigre Quick Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tigre/inst/doc/tigre_quick.R, vignettes/tigre/inst/doc/tigre.R Package: tilingArray Version: 1.36.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 Archs: i386, x64 Title: Transcript mapping with high-density oligonucleotide tiling arrays Description: The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations. biocViews: Microarray, OneChannel, Preprocessing, Visualization Author: Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie Maintainer: Zhenyu Xu MD5sum: 7563316cd9646c75426043a043a47917 source.ver: src/contrib/tilingArray_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/tilingArray_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/tilingArray_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tilingArray_1.36.0.tgz vignettes: vignettes/tilingArray/inst/doc/assessNorm.pdf, vignettes/tilingArray/inst/doc/costMatrix.pdf, vignettes/tilingArray/inst/doc/findsegments.pdf, vignettes/tilingArray/inst/doc/plotAlongChrom.pdf, vignettes/tilingArray/inst/doc/segmentation.pdf vignetteTitles: Normalisation with the normalizeByReference function in the tilingArray package, Supplement. Calculation of the cost matrix, Introduction to using the segment function to fit a piecewise constant curve, Introduction to the plotAlongChrom function, Segmentation demo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tilingArray/inst/doc/assessNorm.R, vignettes/tilingArray/inst/doc/costMatrix.R, vignettes/tilingArray/inst/doc/findsegments.R, vignettes/tilingArray/inst/doc/plotAlongChrom.R, vignettes/tilingArray/inst/doc/segmentation.R dependsOnMe: ADaCGH2 importsMe: snapCGH Package: timecourse Version: 1.30.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL Title: Statistical Analysis for Developmental Microarray Time Course Data Description: Functions for data analysis and graphical displays for developmental microarray time course data. biocViews: Microarray, TimeCourse, DifferentialExpression Author: Yu Chuan Tai Maintainer: Yu Chuan Tai URL: http://www.bioconductor.org MD5sum: 57883de8b544487bbb7cba6f5bd08ee7 source.ver: src/contrib/timecourse_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/timecourse_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/timecourse_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/timecourse_1.30.0.tgz vignettes: vignettes/timecourse/inst/doc/timecourse.pdf vignetteTitles: timecourse manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/timecourse/inst/doc/timecourse.R Package: tkWidgets Version: 1.36.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 Title: R based tk widgets Description: Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. biocViews: Infrastructure Author: J. Zhang Maintainer: J. Zhang MD5sum: 17fce848671339e6b39416a04e9f1d85 source.ver: src/contrib/tkWidgets_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/tkWidgets_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/tkWidgets_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tkWidgets_1.36.0.tgz vignettes: vignettes/tkWidgets/inst/doc/importWizard.pdf, vignettes/tkWidgets/inst/doc/tkWidgets.pdf vignetteTitles: tkWidgets importWizard, tkWidgets contents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tkWidgets/inst/doc/importWizard.R, vignettes/tkWidgets/inst/doc/tkWidgets.R dependsOnMe: cosmoGUI, oneChannelGUI importsMe: Mfuzz, OLINgui suggestsMe: affy, affyQCReport, annotate, Biobase, genefilter, marray Package: topGO Version: 2.10.0 Depends: R (>= 2.10.0), methods, graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: methods, graph, Biobase, SparseM, AnnotationDbi, lattice Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL Title: topGO: Enrichment analysis for Gene Ontology Description: topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. biocViews: Microarray,Bioinformatics,Visualization Author: Adrian Alexa, Jorg Rahnenfuhrer Maintainer: Adrian Alexa MD5sum: 31a11437737b6ff16f0d376010e72f4b source.ver: src/contrib/topGO_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/topGO_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/topGO_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/topGO_2.10.0.tgz vignettes: vignettes/topGO/inst/doc/topGO_classes_v3.pdf, vignettes/topGO/inst/doc/topGO.pdf vignetteTitles: topGO_classes_v3.pdf, topGO hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/topGO/inst/doc/topGO.R dependsOnMe: RNAither suggestsMe: Ringo Package: TransView Version: 1.0.7 Depends: methods,GenomicRanges Imports: Rsamtools,zlibbioc,gplots,IRanges LinkingTo: Rsamtools Suggests: RUnit,pasillaBamSubset License: GPL-3 Archs: i386, x64 Title: Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets. Description: This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq. biocViews: Bioinformatics,DNAMethylation,GeneExpression,Transcription, Microarray,Sequencing,HighThroughputSequencing,ChIPseq,RNAseq, Methylseq,DataImport,Visualization,Clustering,MultipleComparisons Author: Julius Muller Maintainer: Julius Muller URL: http://bioconductor.org/packages/release/bioc/html/TransView.html MD5sum: 4ebe4001910e39d83fdaded5aac8d50e source.ver: src/contrib/TransView_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/TransView_1.0.7.zip win64.binary.ver: bin/windows64/contrib/2.15/TransView_1.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TransView_1.0.7.tgz vignettes: vignettes/TransView/inst/doc/TransView.pdf vignetteTitles: An introduction to TransView hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TransView/inst/doc/TransView.R Package: triform Version: 1.0.0 Depends: R (>= 2.11.0), IRanges, yaml Imports: IRanges, yaml, BiocGenerics Suggests: RUnit License: GPL-2 Title: Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data Description: The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics. biocViews: Sequencing, ChIPseq Author: Karl Kornacker Developer [aut], Tony Håndstad Developer [aut, cre] Maintainer: Tony Håndstad Developer MD5sum: f67ef3d26b2b70f1cb3aee14562eab35 source.ver: src/contrib/triform_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/triform_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/triform_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/triform_1.0.0.tgz vignettes: vignettes/triform/inst/doc/triform.pdf vignetteTitles: Triform users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/triform/inst/doc/triform.R Package: trigger Version: 1.4.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 Archs: i386, x64 Title: Transcriptional Regulatory Inference from Genetics of Gene ExpRession Description: This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest. biocViews: GeneExpression, SNP, GeneticVariability, Microarray, Genetics Author: Lin S. Chen , Dipen P. Sangurdekar and John D. Storey Maintainer: John D. Storey MD5sum: 466aff98f2146bbe14e5ddfccbd2b03a source.ver: src/contrib/trigger_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/trigger_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/trigger_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/trigger_1.4.0.tgz vignettes: vignettes/trigger/inst/doc/net50.pdf, vignettes/trigger/inst/doc/trigger.pdf vignetteTitles: net50.pdf, Trigger Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/trigger/inst/doc/trigger.R Package: tspair Version: 1.16.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 Archs: i386, x64 Title: Top Scoring Pairs for Microarray Classification Description: These functions calculate the pair of genes that show the maximum difference in ranking between two user specified groups. This "top scoring pair" maximizes the average of sensitivity and specificity over all rank based classifiers using a pair of genes in the data set. The advantage of classifying samples based on only the relative rank of a pair of genes is (a) the classifiers are much simpler and often more interpretable than more complicated classification schemes and (b) if arrays can be classified using only a pair of genes, PCR based tests could be used for classification of samples. See the references for the tspcalc() function for references regarding TSP classifiers. biocViews: Microarray, Bioinformatics Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek MD5sum: 4f84adf894961f3be7d453bb605113c4 source.ver: src/contrib/tspair_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/tspair_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/tspair_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tspair_1.16.0.tgz vignettes: vignettes/tspair/inst/doc/tsp1.pdf, vignettes/tspair/inst/doc/tsp.pdf vignetteTitles: tsp1.pdf, tspTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tspair/inst/doc/tsp.R dependsOnMe: stepwiseCM Package: TSSi Version: 1.4.0 Depends: R (>= 2.13.2), BiocGenerics (>= 0.3.2) Imports: BiocGenerics, methods, Hmisc, minqa, stats, Biobase (>= 0.3.2), plyr, IRanges Suggests: rtracklayer Enhances: multicore License: GPL-3 Archs: i386, x64 Title: Transcription Start Site Identification Description: Identify and normalize transcription start sites in high-throughput sequencing data. biocViews: Sequencing, HighThroughputSequencing, RNAseq, Genetics, Preprocessing Author: Clemens Kreutz, Julian Gehring Maintainer: Julian Gehring URL: http://julian-gehring.github.com/TSSi/ MD5sum: 7420a6e03f30fb5964a42cf3164d5021 source.ver: src/contrib/TSSi_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TSSi_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TSSi_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TSSi_1.4.0.tgz vignettes: vignettes/TSSi/inst/doc/TSSi.pdf vignetteTitles: Introduction to the TSSi package: Identification of Transcription Start Sites hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TSSi/inst/doc/TSSi.R Package: TurboNorm Version: 1.6.2 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: affydata, affy, lattice License: LGPL Title: A fast scatterplot smoother suitable for microarray normalization Description: A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available. biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, DNAMethylation, CpGIsland Author: Maarten van Iterson and Chantal van Leeuwen Maintainer: Maarten van Iterson URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html MD5sum: 6db4b7faab10013d4d721397a705a382 source.ver: src/contrib/TurboNorm_1.6.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/TurboNorm_1.6.2.zip win64.binary.ver: bin/windows64/contrib/2.15/TurboNorm_1.6.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TurboNorm_1.6.2.tgz vignettes: vignettes/TurboNorm/inst/doc/turbonorm.pdf vignetteTitles: TurboNorm Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TurboNorm/inst/doc/turbonorm.R Package: tweeDEseq Version: 1.4.1 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) Archs: i386, x64 Title: RNA-seq data analysis using the Poisson-Tweedie family of distributions Description: Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. biocViews: Statistics, DifferentialExpression, HighThroughputSequencing, RNAseq Author: Juan R Gonzalez and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm MD5sum: 3cda9b54f8936cbe473039a4be80c5f4 source.ver: src/contrib/tweeDEseq_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/tweeDEseq_1.4.1.zip win64.binary.ver: bin/windows64/contrib/2.15/tweeDEseq_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tweeDEseq_1.4.1.tgz vignettes: vignettes/tweeDEseq/inst/doc/tweeDEseq.pdf vignetteTitles: tweeDEseq: analysis of RNA-seq data using the Poisson-Tweedie family of distributions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tweeDEseq/inst/doc/tweeDEseq.R Package: twilight Version: 1.34.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) Archs: i386, x64 Title: Estimation of local false discovery rate Description: In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package 'twilight' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished. biocViews: Microarray, Bioinformatics, DifferentialExpression, MultipleComparisons Author: Stefanie Scheid Maintainer: Stefanie Scheid URL: http://compdiag.molgen.mpg.de/software/twilight.shtml MD5sum: fa6c201d51c8f60b90a0c842911c56c8 source.ver: src/contrib/twilight_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/twilight_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/twilight_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/twilight_1.34.0.tgz vignettes: vignettes/twilight/inst/doc/bcb_logo.pdf, vignettes/twilight/inst/doc/tr_2004_01.pdf vignetteTitles: bcb_logo.pdf, Estimation of Local False Discovery Rates hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/twilight/inst/doc/tr_2004_01.R dependsOnMe: OrderedList importsMe: OrderedList Package: TypeInfo Version: 1.24.0 Depends: methods Suggests: Biobase License: BSD Title: Optional Type Specification Prototype Description: A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions. Additionally, the arguments in a call to a typed function can be validated using the type specifications. We allow types to be specified as either i) by class name using either inheritance - is(x, className), or strict instance of - class(x) %in% className, or ii) a dynamic test given as an R expression which is evaluated at run-time. More precise information and interesting tests can be done via ii), but it is harder to use this information as meta-data as it requires more effort to interpret it and it is of course run-time information. It is typically more meaningful. biocViews: Infrastructure Author: Duncan Temple Lang Robert Gentleman () Maintainer: Duncan Temple Lang MD5sum: 8046a8b1b5406d8217d7edd8ab1e8fdc source.ver: src/contrib/TypeInfo_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TypeInfo_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TypeInfo_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TypeInfo_1.24.0.tgz vignettes: vignettes/TypeInfo/inst/doc/TypeInfoNews.pdf vignetteTitles: TypeInfo R News hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TypeInfo/inst/doc/TypeInfoNews.R htmlDocs: vignettes/TypeInfo/inst/doc/outline.html dependsOnMe: RWebServices Package: VanillaICE Version: 1.20.3 Depends: R (>= 2.14.0) Imports: stats, utils, methods, Biobase, oligoClasses (>= 1.19.36),lattice, IRanges (>= 1.13.22), grid, msm, crlmm, foreach, GenomicRanges, matrixStats Suggests: genomewidesnp6Crlmm, hapmapsnp6, RColorBrewer, genefilter, RSQLite, foreach, RUnit, pd.mapping50k.hind240, SNPchip (>= 2.2.0) Enhances: DNAcopy, crlmm License: LGPL-2 Archs: i386, x64 Title: A Hidden Markov Model for high throughput genotyping arrays Description: Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays biocViews: Bioinformatics, CopyNumberVariants, SNP, GeneticVariability, Visualization Author: Robert Scharpf , Kevin Scharpf, and Ingo Ruczinski Maintainer: Robert Scharpf MD5sum: 5b29803bc26952d3a9b2c99b328c1d53 source.ver: src/contrib/VanillaICE_1.20.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/VanillaICE_1.20.3.zip win64.binary.ver: bin/windows64/contrib/2.15/VanillaICE_1.20.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/VanillaICE_1.20.3.tgz vignettes: vignettes/VanillaICE/inst/doc/crlmmDownstream.pdf, vignettes/VanillaICE/inst/doc/VanillaICE.pdf vignetteTitles: crlmmDownstream, VanillaICE Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VanillaICE/inst/doc/crlmmDownstream.R, vignettes/VanillaICE/inst/doc/VanillaICE.R importsMe: MinimumDistance suggestsMe: oligoClasses Package: VariantAnnotation Version: 1.4.12 Depends: R (>= 2.8.0), methods, GenomicRanges (>= 1.9.56), Rsamtools (>= 1.9.4), IRanges (>= 1.15.48) Imports: methods, BiocGenerics (>= 0.1.0), IRanges, Biobase (>= 2.15.1), Rsamtools (>= 1.9.4), AnnotationDbi (>= 1.17.11), Biostrings (>= 2.25.2), zlibbioc, BSgenome, GenomicFeatures (>= 1.9.35), DBI LinkingTo: IRanges, Biostrings, Rsamtools Suggests: RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats License: Artistic-2.0 Archs: i386, x64 Title: Annotation of Genetic Variants Description: Annotate variants with respect to location and amino acid coding biocViews: DataImport, Sequencing, HighThroughputSequencing, SNP, Annotation, Genetics, Homo_sapiens Author: Valerie Obenchain, Martin Morgan, Michael Lawrence Maintainer: Valerie Obenchain MD5sum: b8054ca9398a2671a28052ad329f04dc source.ver: src/contrib/VariantAnnotation_1.4.12.tar.gz win.binary.ver: bin/windows/contrib/2.15/VariantAnnotation_1.4.12.zip win64.binary.ver: bin/windows64/contrib/2.15/VariantAnnotation_1.4.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/VariantAnnotation_1.4.12.tgz vignettes: vignettes/VariantAnnotation/inst/doc/VariantAnnotation.pdf vignetteTitles: Introduction to VariantAnnotation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VariantAnnotation/inst/doc/VariantAnnotation.R dependsOnMe: VariantTools importsMe: FunciSNP, ggbio, GGtools, gmapR, R453Plus1Toolbox, VariantTools suggestsMe: GenomicRanges, gmapR, GWASTools Package: VariantTools Version: 1.0.1 Depends: IRanges (>= 1.15.44), GenomicRanges (>= 1.9.52), VariantAnnotation (>= 1.3.20), methods Imports: IRanges, Rsamtools (>= 1.9.31), GenomicRanges, BiocGenerics, Biostrings, parallel, gmapR (>= 0.99.28), GenomicFeatures, VariantAnnotation, methods Suggests: RUnit, LungCancerLines (>= 0.0.6) License: Artistic-2.0 Title: Tools for Working with Genetic Variants Description: Tools for Tools for detecting, filtering, calling, comparing and plotting variants. biocViews: Genetics, GeneticVariability, HighThroughputSequencing Author: Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman Maintainer: Michael Lawrence MD5sum: 1b9e5f0c9fac87d43ad315a833c742ea source.ver: src/contrib/VariantTools_1.0.1.tar.gz vignettes: vignettes/VariantTools/inst/doc/SNVsOmuC.pdf, vignettes/VariantTools/inst/doc/VariantTools.pdf vignetteTitles: SNVsOmuC.pdf, Introduction to VariantTools hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VariantTools/inst/doc/VariantTools.R Package: vbmp Version: 1.26.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) Title: Variational Bayesian Multinomial Probit Regression Description: Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination. biocViews: Bioinformatics,Classification Author: Nicola Lama , Mark Girolami Maintainer: Nicola Lama URL: http://bioinformatics.oxfordjournals.org/cgi/content/short/btm535v1 MD5sum: 66df78e52188b52adf10129032b510ce source.ver: src/contrib/vbmp_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/vbmp_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/vbmp_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/vbmp_1.26.0.tgz vignettes: vignettes/vbmp/inst/doc/vbmp.pdf vignetteTitles: vbmp Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vbmp/inst/doc/vbmp.R Package: Vega Version: 1.6.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Title: An R package for copy number data segmentation Description: Vega (Variational Estimator for Genomic Aberrations) is an algorithm that adapts a very popular variational model (Mumford and Shah) used in image segmentation so that chromosomal aberrant regions can be efficiently detected. biocViews: aCGH, CopyNumberVariants Author: Sandro Morganella Maintainer: Sandro Morganella MD5sum: 7d76d43137b98eb9353227e2a4e24110 source.ver: src/contrib/Vega_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Vega_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Vega_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Vega_1.6.0.tgz vignettes: vignettes/Vega/inst/doc/Vega.pdf vignetteTitles: Vega hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Vega/inst/doc/Vega.R Package: VegaMC Version: 2.2.0 Depends: R (>= 2.10.0), biomaRt, Biobase, genoset Imports: methods License: GPL-2 Archs: i386, x64 Title: VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer Description: This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported. biocViews: Bioinformatics, aCGH, CopyNumberVariants Author: S. Morganella and M. Ceccarelli Maintainer: Sandro Morganella MD5sum: 8609d4bc81efde0a6a418e28e508fb60 source.ver: src/contrib/VegaMC_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/VegaMC_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/VegaMC_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/VegaMC_2.2.0.tgz vignettes: vignettes/VegaMC/inst/doc/VegaMC.pdf vignetteTitles: VegaMC hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VegaMC/inst/doc/VegaMC.R Package: virtualArray Version: 1.2.1 Depends: R (>= 2.3.0), methods, plyr, preprocessCore Imports: affy, affyPLM, AnnotationDbi, Biobase, gcrma, GEOquery, graphics, methods, reshape2, stats, utils Suggests: affydata, plier, limma, lumi, org.Hs.eg.db Enhances: parallel License: GPL-3 Title: Build virtual array from different microarray platforms Description: This package permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analysing the resulting virtual array. biocViews: Microarray, OneChannel, DataImport, Preprocessing, Bioinformatics, MultipleComparisons Author: Andreas Heider Maintainer: Andreas Heider MD5sum: 80d81ba648d88ca00c03d765c2273b96 source.ver: src/contrib/virtualArray_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/virtualArray_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/virtualArray_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/virtualArray_1.2.1.tgz vignettes: vignettes/virtualArray/inst/doc/virtualArray-016.pdf, vignettes/virtualArray/inst/doc/virtualArray-022.pdf, vignettes/virtualArray/inst/doc/virtualArray-023.pdf, vignettes/virtualArray/inst/doc/virtualArray.pdf vignetteTitles: virtualArray-016.pdf, virtualArray-022.pdf, virtualArray-023.pdf, virtualArray Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/virtualArray/inst/doc/virtualArray.R Package: vsn Version: 3.26.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: methods, affy (>= 1.23.4), limma, lattice Suggests: affydata, hgu95av2cdf License: Artistic-2.0 Archs: i386, x64 Title: Variance stabilization and calibration for microarray data Description: The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references (see vignette). The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. biocViews: Microarray, OneChannel, TwoChannel, Preprocessing Author: Wolfgang Huber, with contributions from Anja von Heydebreck. Many comments and suggestions by users are acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth. Maintainer: Wolfgang Huber URL: http://www.r-project.org, http://www.ebi.ac.uk/huber MD5sum: dc3543c14aa178d9f7a3fa4ee45fb43c source.ver: src/contrib/vsn_3.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/vsn_3.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/vsn_3.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/vsn_3.26.0.tgz vignettes: vignettes/vsn/inst/doc/convergence2.pdf, vignettes/vsn/inst/doc/likelihoodcomputations.pdf, vignettes/vsn/inst/doc/vsn.pdf vignetteTitles: Verifying and assessing the performance with simulated data, Likelihood Calculations for vsn, Introduction to vsn hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vsn/inst/doc/convergence2.R, vignettes/vsn/inst/doc/likelihoodcomputations.R, vignettes/vsn/inst/doc/vsn.R dependsOnMe: affyPara, cellHTS2, LVSmiRNA, MmPalateMiRNA, webbioc importsMe: arrayQualityMetrics, imageHTS, MSnbase, Ringo, tilingArray suggestsMe: adSplit, Agi4x44PreProcess, beadarray, BiocCaseStudies, cellHTS, DESeq, GlobalAncova, globaltest, limma, lumi, twilight Package: waveTiling Version: 1.0.0 Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, IRanges Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart12 License: GPL (>=2) Archs: i386, x64 Title: Wavelet-Based Models for Tiling Array Transcriptome Analysis Description: This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models. biocViews: MicroArray, DifferentialExpression, TimeCourse, GeneExpression Author: Kristof De Beuf , Peter Pipelers and Lieven Clement Maintainer: Kristof De Beuf URL: https://r-forge.r-project.org/projects/wavetiling/ MD5sum: f39850a950cf0e1c14cd1f98e656fc05 source.ver: src/contrib/waveTiling_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/waveTiling_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/waveTiling_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/waveTiling_1.0.0.tgz vignettes: vignettes/waveTiling/inst/doc/waveTiling-vignette.pdf vignetteTitles: The waveTiling package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/waveTiling/inst/doc/waveTiling-vignette.R Package: weaver Version: 1.24.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 Title: Tools and extensions for processing Sweave documents Description: This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included. biocViews: Infrastructure Author: Seth Falcon Maintainer: Seth Falcon MD5sum: 3c4910eed517a0da223a0693deb78089 source.ver: src/contrib/weaver_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/weaver_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/weaver_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/weaver_1.24.0.tgz vignettes: vignettes/weaver/inst/doc/weaver_howTo.pdf vignetteTitles: Using weaver to process Sweave documents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/weaver/inst/doc/weaver_howTo.R suggestsMe: BiocCaseStudies Package: webbioc Version: 1.30.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocInstaller License: GPL (>= 2) Title: Bioconductor Web Interface Description: An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.) biocViews: Infrastructure, Microarray, OneChannel, DifferentialExpression Author: Colin A. Smith Maintainer: Colin A. Smith URL: http://www.bioconductor.org/ SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm MD5sum: aa9ae77b109ed4c093293d89de17c730 source.ver: src/contrib/webbioc_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/webbioc_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/webbioc_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/webbioc_1.30.0.tgz vignettes: vignettes/webbioc/inst/doc/demoscript.pdf, vignettes/webbioc/inst/doc/webbioc.pdf vignetteTitles: webbioc Demo Script, webbioc Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/webbioc/inst/doc/demoscript.R, vignettes/webbioc/inst/doc/webbioc.R Package: widgetTools Version: 1.36.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL Title: Creates an interactive tcltk widget Description: This packages contains tools to support the construction of tcltk widgets biocViews: Infrastructure Author: Jianhua Zhang Maintainer: Jianhua Zhang MD5sum: b9c03198f14965718e34823e6b24eb8c source.ver: src/contrib/widgetTools_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/widgetTools_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.15/widgetTools_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/widgetTools_1.36.0.tgz vignettes: vignettes/widgetTools/inst/doc/widget.pdf, vignettes/widgetTools/inst/doc/widgetTools.pdf vignetteTitles: widget.pdf, widgetTools Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/widgetTools/inst/doc/widgetTools.R dependsOnMe: tkWidgets importsMe: OLINgui suggestsMe: affy Package: xcms Version: 1.34.0 Depends: R (>= 1.9.0), methods, mzR (>= 1.1.6) Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>= 1.5.2), RANN, snow, RUnit Enhances: Rgraphviz, XML, KEGGSOAP License: GPL (>= 2) Archs: i386, x64 Title: LC/MS and GC/MS Data Analysis Description: Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling. biocViews: MassSpectrometry, Metabolomics Author: Colin A. Smith , Ralf Tautenhahn , Steffen Neumann , Paul Benton Maintainer: Ralf Tautenhahn URL: http://metlin.scripps.edu/download/ MD5sum: 44a5e9bd37787729d310b47e8d5a661a source.ver: src/contrib/xcms_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/xcms_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/xcms_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/xcms_1.34.0.tgz vignettes: vignettes/xcms/inst/doc/FlowChart.pdf, vignettes/xcms/inst/doc/xcmsDirect.pdf, vignettes/xcms/inst/doc/xcmsInstall.pdf, vignettes/xcms/inst/doc/xcmsMSn.pdf, vignettes/xcms/inst/doc/xcmsPreprocess.pdf vignetteTitles: FlowChart.pdf, Grouping FTICR-MS data with xcms, Installation Instructions for xcms, Processing Tandem-MS and MS$^n$ data with xcms, LC/MS Preprocessing and Analysis with xcms hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/xcms/inst/doc/xcmsDirect.R, vignettes/xcms/inst/doc/xcmsInstall.R, vignettes/xcms/inst/doc/xcmsMSn.R, vignettes/xcms/inst/doc/xcmsPreprocess.R dependsOnMe: CAMERA, flagme importsMe: CAMERA, Risa suggestsMe: MassSpecWavelet Package: XDE Version: 2.4.1 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), methods, graphics Imports: Biobase, BiocGenerics, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils, mvtnorm Suggests: siggenes, genefilter, MASS, RColorBrewer, GeneMeta, RUnit Enhances: coda License: LGPL-2 Archs: i386, x64 Title: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression Description: Multi-level model for cross-study detection of differential gene expression. biocViews: Microarray, Bioinformatics, DifferentialExpression Author: R.B. Scharpf, G. Parmigiani, A.B. Nobel, and H. Tjelmeland Maintainer: Robert Scharpf MD5sum: 84a1f53230a603279c54e23e70bad38b source.ver: src/contrib/XDE_2.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/XDE_2.4.1.zip win64.binary.ver: bin/windows64/contrib/2.15/XDE_2.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/XDE_2.4.1.tgz vignettes: vignettes/XDE/inst/doc/XdeParameterClass.pdf, vignettes/XDE/inst/doc/XDE.pdf vignetteTitles: XdeParameterClass Vignette, XDE Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/XDE/inst/doc/XdeParameterClass.R, vignettes/XDE/inst/doc/XDE.R Package: xmapbridge Version: 1.16.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 Title: Export plotting files to the xmapBridge for visualisation in X:Map Description: xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format. biocViews: Annotation, ReportWriting, Visualization Author: Tim Yates and Crispin J Miller Maintainer: Tim Yates URL: http://xmap.picr.man.ac.uk, http://www.bioconductor.org MD5sum: 0818bf2b16c15b7cb37ec5eb595fcf59 source.ver: src/contrib/xmapbridge_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/xmapbridge_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/xmapbridge_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/xmapbridge_1.16.0.tgz vignettes: vignettes/xmapbridge/inst/doc/xmapbridge.pdf vignetteTitles: xmapbridge primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/xmapbridge/inst/doc/xmapbridge.R Package: xmapcore Version: 1.12.0 Depends: R (>= 2.8.0), methods, IRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase Suggests: RUnit License: GPL-2 Title: Core access to the xmap database (installed separately) Description: xmapcore is deprecated and will not be supported after Bioconductor release 2.10. It has been superceded by a new package 'annmap'. xmapcore allows mapping between genetic features and any available Affymetrix Exon arrays for Homo Sapiens, Mus Musculus, Rattus Norvegicus and Schizosaccharomyces Pombe. biocViews: Annotation, Bioinformatics, Microarray, OneChannel, ReportWriting, Transcription, Visualization Author: Tim Yates Maintainer: Tim Yates URL: http://xmap.picr.man.ac.uk, http://www.bioconductor.org MD5sum: 5bc4718ca8c7a22ead3995d03afcf967 source.ver: src/contrib/xmapcore_1.12.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/xmapcore_1.12.0.tgz vignettes: vignettes/xmapcore/inst/doc/cookbook.pdf, vignettes/xmapcore/inst/doc/INSTALL.pdf, vignettes/xmapcore/inst/doc/SplicingIndexExample.pdf, vignettes/xmapcore/inst/doc/xmapcore.pdf vignetteTitles: cookbook.pdf, xmapcore installation instruction, SplicingIndexExample.pdf, xmapcore primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/xmapcore/inst/doc/INSTALL.R, vignettes/xmapcore/inst/doc/xmapcore.R dependsOnMe: rnaSeqMap Package: xps Version: 1.18.1 Depends: R (>= 2.6.0), methods, utils Suggests: tools License: GPL (>= 2.0) Title: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays Description: The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch. biocViews: ExonArray, GeneExpression, Microarray, OneChannel, DataImport, Preprocessing, Transcription, DifferentialExpression Author: Christian Stratowa, Vienna, Austria Maintainer: Christian Stratowa SystemRequirements: root_v5.32.01 - See README file for installation instructions. MD5sum: 411babdfc161d913f62b695106145eec source.ver: src/contrib/xps_1.18.1.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/xps_1.18.1.tgz vignettes: vignettes/xps/inst/doc/APTvsXPS.pdf, vignettes/xps/inst/doc/xpsClasses.pdf, vignettes/xps/inst/doc/xps.pdf, vignettes/xps/inst/doc/xpsPreprocess.pdf vignetteTitles: 3. XPS Vignette: Comparison APT vs XPS, 2. XPS Vignette: Classes, 1. XPS Vignette: Overview, 4. XPS Vignette: Function express() hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/xps/inst/doc/APTvsXPS.R, vignettes/xps/inst/doc/xpsClasses.R, vignettes/xps/inst/doc/xpsPreprocess.R, vignettes/xps/inst/doc/xps.R Package: yaqcaffy Version: 1.18.0 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 Title: Affymetrix expression data quality control and reproducibility analysis Description: Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. biocViews: Microarray,OneChannel,QualityControl,ReportWriting Author: Laurent Gatto Maintainer: Laurent Gatto MD5sum: b3ed0b447cd663a32b6111f2fbc47d40 source.ver: src/contrib/yaqcaffy_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/yaqcaffy_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/yaqcaffy_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/yaqcaffy_1.18.0.tgz vignettes: vignettes/yaqcaffy/inst/doc/yaqcaffy.pdf vignetteTitles: yaqcaffy: Affymetrix quality control and MAQC reproducibility hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yaqcaffy/inst/doc/yaqcaffy.R Package: zlibbioc Version: 1.4.0 License: Artistic-2.0 + file LICENSE Archs: i386, x64 Title: An R packaged zlib-1.2.5 Description: This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use. biocViews: Infrastructure Author: Martin Morgan Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html MD5sum: f598c1ffbc8453a4186f562fa8b86e55 source.ver: src/contrib/zlibbioc_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/zlibbioc_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/zlibbioc_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/zlibbioc_1.4.0.tgz vignettes: vignettes/zlibbioc/inst/doc/UsingZlibbioc.pdf vignetteTitles: Using zlibbioc C libraries hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/zlibbioc/inst/doc/UsingZlibbioc.R dependsOnMe: BitSeq importsMe: affy, affyio, affyPLM, DiffBind, makecdfenv, oligo, rhdf5, Rsamtools, rtracklayer, seqbias, ShortRead, Starr, VariantAnnotation