Package: RBGL Version: 1.7.0 Depends: graph Title: Test interface to boost C++ graph lib Description: demo of interface with full copy of all hpp defining boost biocViews: GraphsAndNetworks Author: Vince Carey , Li Long Maintainer: Li Long URL: http://www.bioconductor.org License: LGPL source.ver: src/contrib/RBGL_1.7.0.tar.gz vignettes: vignettes/RBGL/inst/doc/RBGL-004.pdf, vignettes/RBGL/inst/doc/RBGL-005.pdf, vignettes/RBGL/inst/doc/RBGL-006.pdf, vignettes/RBGL/inst/doc/RBGL-011.pdf, vignettes/RBGL/inst/doc/RBGL-012.pdf, vignettes/RBGL/inst/doc/RBGL-016.pdf, vignettes/RBGL/inst/doc/RBGL-017.pdf, vignettes/RBGL/inst/doc/RBGL.pdf, vignettes/RBGL/inst/doc/filedep.pdf Package: Rgraphviz Version: 1.9.0 Depends: R (>= 2.1.0), graph Suggests: Biobase, geneplotter, fibroEset, hgu95av2 Title: Provides plotting capabilities for R graph objects Description: Interfaces R with the AT&T GraphViz library to provide the ability for plotting R graph objects from the graph package biocViews: GraphsAndNetworks Author: Jeff Gentry Maintainer: Jeff Gentry License: LGPL SystemRequirements: Graphviz version >= 1.12 source.ver: src/contrib/Rgraphviz_1.9.0.tar.gz vignettes: vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf, vignettes/Rgraphviz/inst/doc/layingOutPathways.pdf Package: Ruuid Version: 1.9.0 Depends: R (>= 2.1), methods Title: Ruuid: Provides Universally Unique ID values Description: A package to provide UUID values in R Author: R. Gentleman Maintainer: R. Gentleman License: LGPL source.ver: src/contrib/Ruuid_1.9.0.tar.gz vignettes: vignettes/Ruuid/inst/doc/Ruuid.pdf Package: aCGH Version: 1.5.0 Depends: R (>= 1.8.0), cluster, survival, multtest, sma 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. Author: Jane Fridlyand , Peter Dimitrov Maintainer: Jane Fridlyand License: GPL source.ver: src/contrib/aCGH_1.5.0.tar.gz win.binary.ver: bin/windows/contrib/2.3/aCGH_1.4.0.zip vignettes: vignettes/aCGH/inst/doc/aCGH.pdf Package: affxparser Version: 1.3.0 Depends: R (>= 2.0), Biobase Suggests: affy Title: Affymetrix File Parsing SDK Description: Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR) biocViews: DataImport Author: James Bullard, Kasper Daniel Hansen Maintainer: James Bullard License: LGPL-2 source.ver: src/contrib/affxparser_1.3.0.tar.gz Package: affy Version: 1.9.1 Depends: R (>= 2.0.1), Biobase (>= 1.5.0), methods, utils Suggests: tkWidgets (>= 1.2.2), affydata Title: Methods for Affymetrix Oligonucleotide Arrays Description: The package contains functions for exploratory oligonucleotide array analysis. The dependance to 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 License: LGPL version 2 or newer source.ver: src/contrib/affy_1.9.1.tar.gz win.binary.ver: bin/windows/contrib/2.3/affy_1.8.1.zip vignettes: vignettes/affy/inst/doc/affy.pdf, vignettes/affy/inst/doc/builtinMethods.pdf, vignettes/affy/inst/doc/customMethods.pdf, vignettes/affy/inst/doc/dealing_with_cdfenvs.pdf, vignettes/affy/inst/doc/vim.pdf Package: affycomp Version: 1.7.0 Depends: R (>= 1.8.1), Biobase (>= 1.1.0) 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. Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley , Maintainer: Rafael A. Irizarry License: GPL version 2 or newer source.ver: src/contrib/affycomp_1.7.0.tar.gz win.binary.ver: bin/windows/contrib/2.3/affycomp_1.6.0.zip vignettes: vignettes/affycomp/inst/doc/affycomp.pdf Package: affydata Version: 1.7.0 Depends: R (>= 1.6.2), affy (>= 1.2) Suggests: hgu95av2cdf, hgu133acdf Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. Author: Bioconductor Maintainer: Laurent License: GPL version 2 or newer source.ver: src/contrib/affydata_1.7.0.tar.gz win.binary.ver: bin/windows/contrib/2.3/affydata_1.6.0.zip vignettes: vignettes/affydata/inst/doc/affydata.pdf Package: affylmGUI Version: 1.5.0 Depends: limma, tcltk, affy Suggests: tkrplot, affyPLM, R2HTML, xtable 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, Statistics, DifferentialExpression, MultipleComparisons Author: James Wettenhall and Ken Simpson Division of Genetics and Bioinformatics, WEHI. Maintainer: Keith Satterley URL: http://bioinf.wehi.edu.au/affylmGUI/ License: GPL version 2 or newer source.ver: src/contrib/affylmGUI_1.5.0.tar.gz win.binary.ver: bin/windows/contrib/2.3/affylmGUI_1.4.0.zip vignettes: vignettes/affylmGUI/inst/doc/affylmGUI.pdf, vignettes/affylmGUI/inst/doc/extract.pdf Package: affypdnn Version: 1.5.0 Depends: R (>= 1.9.0), affy (>= 1.5), affydata, hgu95av2probe 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. 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 License: LGPL source.ver: src/contrib/affypdnn_1.5.0.tar.gz win.binary.ver: bin/windows/contrib/2.3/affypdnn_1.4.0.zip Package: graph Version: 1.9.0 Depends: R (>= 2.1.0), cluster, Ruuid Suggests: SparseM (>= 0.36), XML 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 Maintainer: R. Gentleman License: LGPL source.ver: src/contrib/graph_1.9.0.tar.gz vignettes: vignettes/graph/inst/doc/clusterGraph.pdf, vignettes/graph/inst/doc/graph.pdf