Package: a4 Version: 1.52.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db License: GPL-3 MD5sum: 5e0a21e1348ae673db7655b14e91af84 Package: a4Base Version: 1.52.0 Depends: a4Preproc, a4Core Imports: methods, graphics, grid, Biobase, annaffy, mpm, genefilter, limma, multtest, glmnet, gplots Suggests: Cairo, ALL, hgu95av2.db, nlcv Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 72ad1974631277cce6897126a8579e43 Package: a4Classif Version: 1.52.0 Depends: a4Core, a4Preproc Imports: methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils, graphics, stats Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: 51e57ce861006edadf448d938a3d6c95 Package: a4Core Version: 1.52.0 Imports: Biobase, glmnet, methods, stats Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 8faa903020fc8fa2b1477828f9f1fd7b Package: a4Preproc Version: 1.52.0 Imports: BiocGenerics, Biobase Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: 382b606b4c2e61ba3ae20f423dbeccb1 Package: a4Reporting Version: 1.52.0 Imports: methods, xtable Suggests: knitr, rmarkdown License: GPL-3 MD5sum: fe6f2ac0fd341381a2e53230bd377e1d Package: ABarray Version: 1.72.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL MD5sum: bb2a18aca1380bbaf80901d64c74af5c Package: abseqR Version: 1.22.0 Depends: R (>= 3.5.0) Imports: ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr, flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra, rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly, BiocStyle, stringr, utils, methods, grDevices, stats, tools, graphics Suggests: testthat License: GPL-3 | file LICENSE MD5sum: f04361de004a912359f070c1956026d3 Package: ABSSeq Version: 1.58.0 Depends: R (>= 2.10), methods Imports: locfit, limma Suggests: edgeR License: GPL (>= 3) MD5sum: f1be65a719fed6b719e87b26a570d6e2 Package: acde Version: 1.34.0 Depends: R(>= 3.3), boot(>= 1.3) Imports: stats, graphics Suggests: BiocGenerics, RUnit License: GPL-3 MD5sum: 6afde2602ae392c0ccfd2cb381c01335 Package: ACE Version: 1.22.0 Depends: R (>= 3.4) Imports: Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices, GenomicRanges Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 7cc4eab736378695ad98171610af51fa Package: aCGH Version: 1.82.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, grDevices, graphics, methods, stats, splines, utils License: GPL-2 MD5sum: 0ce3a300908ed29af399ade83fdc8fb4 Package: ACME Version: 2.60.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics Imports: graphics, stats License: GPL (>= 2) MD5sum: 2fa45b74d2f7a3c1f968581f05ef1917 Package: ADaCGH2 Version: 2.44.0 Depends: R (>= 3.2.0), parallel, ff, GLAD Imports: bit, DNAcopy, tilingArray, waveslim, cluster, aCGH Suggests: CGHregions, Cairo, limma Enhances: Rmpi License: GPL (>= 3) MD5sum: 64caa2e48059ad1b903bd85437c10b62 Package: ADAM Version: 1.20.0 Depends: R(>= 3.5), stats, utils, methods Imports: Rcpp (>= 0.12.18), GO.db (>= 3.6.0), KEGGREST (>= 1.20.2), knitr, pbapply (>= 1.3-4), dplyr (>= 0.7.6), DT (>= 0.4), stringr (>= 1.3.1), SummarizedExperiment (>= 1.10.1) LinkingTo: Rcpp Suggests: testthat, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 8dfcffd5440c307edbe7e6da3b31c54c Package: ADAMgui Version: 1.20.0 Depends: R(>= 3.6), stats, utils, methods, ADAM Imports: GO.db (>= 3.5.0), dplyr (>= 0.7.6), shiny (>= 1.1.0), stringr (>= 1.3.1), stringi (>= 1.2.4), varhandle (>= 2.0.3), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), ggpubr (>= 0.1.8), ggsignif (>= 0.4.0), reshape2 (>= 1.4.3), RColorBrewer (>= 1.1-2), colorRamps (>= 2.3), DT (>= 0.4), data.table (>= 1.11.4), gridExtra (>= 2.3), shinyjs (>= 1.0), knitr, testthat Suggests: markdown, BiocStyle License: GPL (>= 2) MD5sum: c37cbde25870681bb96db0dba06c3dfa Package: adductomicsR Version: 1.20.0 Depends: R (>= 3.6), adductData, ExperimentHub, AnnotationHub Imports: parallel (>= 3.3.2), data.table (>= 1.10.4), OrgMassSpecR (>= 0.4.6), foreach (>= 1.4.3), mzR (>= 2.14.0), ade4 (>= 1.7.6), rvest (>= 0.3.2), pastecs (>= 1.3.18), reshape2 (>= 1.4.2), pracma (>= 2.0.4), DT (>= 0.2), fpc (>= 2.1.10), doSNOW (>= 1.0.14), fastcluster (>= 1.1.22), RcppEigen (>= 0.3.3.3.0), bootstrap (>= 2017.2), smoother (>= 1.1), dplyr (>= 0.7.5), zoo (>= 1.8), stats (>= 3.5.0), utils (>= 3.5.0), graphics (>= 3.5.0), grDevices (>= 3.5.0), methods (>= 3.5.0), datasets (>= 3.5.0) Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat License: Artistic-2.0 MD5sum: 9c29a1ba77aadbfe9ceb60a2dacf54ce Package: ADImpute Version: 1.14.0 Depends: R (>= 4.0) Imports: checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS, Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE MD5sum: 720c661e65df15ce398d84a31087d600 Package: adSplit Version: 1.74.0 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, KEGGREST (>= 1.30.1), multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) MD5sum: 8c81624328606d335af895bdafb377cb Package: adverSCarial Version: 1.2.0 Imports: gtools, S4Vectors, methods, DelayedArray Suggests: knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr, LoomExperiment License: MIT + file LICENSE MD5sum: d7107899dad9ed0347215a3302c2426a Package: AffiXcan Version: 1.22.0 Depends: R (>= 3.6), SummarizedExperiment Imports: MultiAssayExperiment, BiocParallel, crayon Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 5e791c2529a827a6c1e4f513769c8206 Package: affxparser Version: 1.76.0 Depends: R (>= 2.14.0) Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles License: LGPL (>= 2) MD5sum: 5323d1b56abdba28d09510001b833a49 Package: affy Version: 1.82.0 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf License: LGPL (>= 2.0) MD5sum: 37b31c13ff75e02a8e65601203ad230d Package: affycomp Version: 1.80.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) MD5sum: de6da105fbf5acbee27064466f94185e Package: affyContam Version: 1.62.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata Suggests: hgu95av2cdf License: Artistic-2.0 MD5sum: 0abc3c829da67cb8ac97e9f985c4638c Package: affycoretools Version: 1.76.0 Depends: Biobase, methods Imports: affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi, ggplot2, gplots, oligoClasses, ReportingTools, hwriter, lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown License: Artistic-2.0 MD5sum: 705a8aef91e5ef0683aee8379d4864e8 Package: affyILM Version: 1.56.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, Biobase Suggests: AffymetrixDataTestFiles, hgfocusprobe License: GPL-3 MD5sum: a28f6c72641736497e9922e9a4cbfabf Package: affyio Version: 1.74.0 Depends: R (>= 2.6.0) Imports: zlibbioc, methods License: LGPL (>= 2) MD5sum: 01afcac987442a33fc74f5c0beee1ded Package: affylmGUI Version: 1.78.0 Imports: grDevices, graphics, stats, utils, tcltk, tkrplot, limma, affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi, BiocManager, R2HTML, xtable License: GPL (>= 2) MD5sum: b373d708491d2400a49b3fcee5535128 Package: affyPLM Version: 1.80.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0), Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1) Imports: zlibbioc, graphics, grDevices, methods LinkingTo: preprocessCore Suggests: affydata, MASS, hgu95av2cdf License: GPL (>= 2) MD5sum: 442e50705729394415c0f26a1352542b Package: AffyRNADegradation Version: 1.50.0 Depends: R (>= 2.9.0), methods, affy Suggests: AmpAffyExample, hgu133acdf License: GPL-2 MD5sum: f3e33af2f354874ffa732abd4e815285 Package: AGDEX Version: 1.52.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL (>= 2) MD5sum: de56c55971b34275338e5266ef0ad131 Package: aggregateBioVar Version: 1.14.0 Depends: R (>= 4.0) Imports: stats, methods, S4Vectors, SummarizedExperiment, SingleCellExperiment, Matrix, tibble, rlang Suggests: BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis License: GPL-3 MD5sum: c27f2bb59f9a9a967687741d054e1495 Package: agilp Version: 3.36.0 Depends: R (>= 2.14.0) License: GPL-3 MD5sum: c518658c9ad80324d0e0945454165615 Package: AgiMicroRna Version: 2.54.0 Depends: R (>= 2.10),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 MD5sum: 62763b41b2f6d3a71b05802626c1dfde Package: AHMassBank Version: 1.4.0 Depends: R (>= 4.2) Imports: AnnotationHubData (>= 1.5.24) Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown, methods, CompoundDb (>= 1.1.4) License: Artistic-2.0 MD5sum: 83254fa1634ac10f439f26897cdba787 Package: AIMS Version: 1.36.0 Depends: R (>= 2.10), e1071, Biobase Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 06f783895fa56a7ac6523087f18c1e09 Package: airpart Version: 1.12.0 Depends: R (>= 4.1) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, scater, stats, smurf, apeglm (>= 1.13.3), emdbook, mclust, clue, dynamicTreeCut, matrixStats, dplyr, plyr, ggplot2, ComplexHeatmap, forestplot, RColorBrewer, rlang, lpSolve, grid, grDevices, graphics, utils, pbapply Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr License: GPL-2 MD5sum: aabd43473ca2cf5b3f311dbfea90f1b8 Package: alabaster Version: 1.4.0 Depends: alabaster.base Imports: alabaster.matrix, alabaster.ranges, alabaster.se, alabaster.sce, alabaster.spatial, alabaster.string, alabaster.vcf, alabaster.bumpy, alabaster.mae Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: f2aa85e9cde62da68679a58d53e145fd Package: alabaster.base Version: 1.4.2 Imports: alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>= 2.47.6), jsonlite, jsonvalidate, Rcpp LinkingTo: Rcpp, Rhdf5lib Suggests: BiocStyle, rmarkdown, knitr, testthat, digest, Matrix License: MIT + file LICENSE MD5sum: 3a6d32056462b090d06c47149927045e Package: alabaster.bumpy Version: 1.4.0 Depends: BumpyMatrix, alabaster.base Imports: methods, rhdf5, Matrix, BiocGenerics, S4Vectors, IRanges Suggests: BiocStyle, rmarkdown, knitr, testthat, jsonlite License: MIT + file LICENSE MD5sum: 456fd2917ef6c43e939a67dcfc104880 Package: alabaster.files Version: 1.2.0 Depends: alabaster.base, Imports: methods, S4Vectors, BiocGenerics, Rsamtools Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation, rtracklayer, Biostrings License: MIT + file LICENSE MD5sum: f6f8460911cdc2199007ff3726b2c5b4 Package: alabaster.mae Version: 1.4.0 Depends: MultiAssayExperiment, alabaster.base Imports: methods, alabaster.se, S4Vectors, jsonlite, rhdf5 Suggests: testthat, knitr, SummarizedExperiment, BiocParallel, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 045c5f98841af03ecf0baf9ffa892852 Package: alabaster.matrix Version: 1.4.2 Depends: alabaster.base Imports: methods, BiocGenerics, S4Vectors, DelayedArray (>= 0.27.2), S4Arrays, SparseArray, rhdf5 (>= 2.47.1), HDF5Array, Matrix, Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, chihaya, BiocSingular, ResidualMatrix License: MIT + file LICENSE MD5sum: 5f323651397af0b7ad82c8fce186a5c9 Package: alabaster.ranges Version: 1.4.2 Depends: GenomicRanges, alabaster.base Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomeInfoDb, rhdf5 Suggests: testthat, knitr, BiocStyle, jsonlite License: MIT + file LICENSE MD5sum: 9579f3ce28b370883266621c8292a349 Package: alabaster.sce Version: 1.4.0 Depends: SingleCellExperiment, alabaster.base Imports: methods, alabaster.se, jsonlite Suggests: knitr, testthat, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: dbb11afe312d2278d76915c5a4393f06 Package: alabaster.schemas Version: 1.4.0 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: a6a207327b244be17c0ac8ae04798d46 Package: alabaster.se Version: 1.4.1 Depends: SummarizedExperiment, alabaster.base Imports: methods, alabaster.ranges, alabaster.matrix, BiocGenerics, S4Vectors, IRanges, GenomicRanges, jsonlite Suggests: rmarkdown, knitr, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 627106f9da4c8b03c35f5fbf5b7f86d6 Package: alabaster.spatial Version: 1.4.0 Depends: SpatialExperiment, alabaster.base Imports: methods, utils, grDevices, S4Vectors, alabaster.sce, rhdf5 Suggests: testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick, png, digest License: MIT + file LICENSE MD5sum: 4c6800d55593ea9660620b078d166bb0 Package: alabaster.string Version: 1.4.0 Depends: Biostrings, alabaster.base Imports: utils, methods, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, testthat License: MIT + file LICENSE MD5sum: 28341ca966166f7c5e37ce3a6ae16f04 Package: alabaster.vcf Version: 1.4.0 Depends: alabaster.base, VariantAnnotation Imports: methods, S4Vectors, alabaster.se, alabaster.string, Rsamtools Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: eabb6a881f1830bc8125447c775b2337 Package: ALDEx2 Version: 1.36.0 Depends: methods, stats, zCompositions, lattice, latticeExtra Imports: Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest, directlabels Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick License: GPL (>= 3) MD5sum: fd3426e0724001bd92df15de8b1b9394 Package: alevinQC Version: 1.20.0 Depends: R (>= 4.0) Imports: rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0), GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.17.4), cowplot, rlang, Rcpp LinkingTo: Rcpp Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager License: MIT + file LICENSE MD5sum: d27b186e7c1eaba1957488f3415561a5 Package: AllelicImbalance Version: 1.42.0 Depends: R (>= 4.0.0), grid, GenomicRanges (>= 1.31.8), SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6) Imports: methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3), VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>= 1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice, latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: e1ee76a75a571d02d3774ec24ff344e8 Package: AlphaBeta Version: 1.18.0 Depends: R (>= 3.6.0) Imports: dplyr (>= 0.7), data.table (>= 1.10), stringr (>= 1.3), utils (>= 3.6.0), gtools (>= 3.8.0), optimx (>= 2018-7.10), expm (>= 0.999-4), stats (>= 3.6), BiocParallel (>= 1.18), igraph (>= 1.2.4), graphics (>= 3.6), ggplot2 (>= 3.2), grDevices (>= 3.6), plotly (>= 4.9) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: e503eb5ff50b19cda886e000c7e090b3 Package: AlphaMissenseR Version: 1.0.2 Depends: dplyr Imports: rjsoncons (>= 1.0.1), DBI, duckdb (>= 0.9.1), rlang, curl, BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats, methods, whisker Suggests: BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb, AnnotationHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, colorspace, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3ccda192f31f8c8c4d6074b25042acac Package: AlpsNMR Version: 4.6.0 Depends: R (>= 4.2), future (>= 1.10.0) Imports: utils, generics, graphics, stats, grDevices, cli, magrittr (>= 1.5), dplyr (>= 1.1.0), signal (>= 0.7-6), rlang (>= 0.3.0.1), scales (>= 1.2.0), stringr (>= 1.3.1), tibble(>= 1.3.4), tidyr (>= 1.0.0), tidyselect, readxl (>= 1.1.0), purrr (>= 0.2.5), glue (>= 1.2.0), reshape2 (>= 1.4.3), mixOmics (>= 6.22.0), matrixStats (>= 0.54.0), fs (>= 1.2.6), rmarkdown (>= 1.10), speaq (>= 2.4.0), htmltools (>= 0.3.6), pcaPP (>= 1.9-73), ggplot2 (>= 3.1.0), baseline (>= 1.2-1), vctrs (>= 0.3.0), BiocParallel Suggests: BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) License: MIT + file LICENSE MD5sum: e06b6e98c2bfe21f1cfbfdb9fa808dd0 Package: altcdfenvs Version: 2.66.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) MD5sum: a3c2da9963735e9f20b8efb98666869b Package: AMARETTO Version: 1.20.0 Depends: R (>= 3.6), impute, doParallel, grDevices, dplyr, methods, ComplexHeatmap Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr, BiocStyle License: Apache License (== 2.0) + file LICENSE MD5sum: d16b661493f664cbe6e395e6e1481450 Package: AMOUNTAIN Version: 1.30.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: aaa77e22552afcac5302bb6f7d4ff3cd Package: amplican Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), pwalign, data.table (>= 1.10.4-3) Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4), GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 MD5sum: f19e3c85352f1af4ac3d5b1b9fd151b5 Package: Anaquin Version: 2.28.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 851845ece29d9bfdce8b27dd61579f2b Package: ANCOMBC Version: 2.6.0 Depends: R (>= 4.3.0) Imports: mia (>= 1.6.0), stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils Suggests: dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr License: Artistic-2.0 MD5sum: 5cd02f9ba0574f75b06981c437200fb6 Package: AneuFinder Version: 1.32.0 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 08311532386c9fb4cff3fe51859e9dd3 Package: ANF Version: 1.26.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: c0c2b9b783c919bf64eba8e9d89e5c73 Package: animalcules Version: 1.20.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 2e7af12bc1299545243e1d692fb0d272 Package: annaffy Version: 1.76.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: 7fa2f3707376e71b787ec89bfadef31b Package: annmap Version: 1.46.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: 8460f5cc0c7a31127fcb2da6d1673ea9 Package: annotate Version: 1.82.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: d44560a8dd38ef07f1f4a9359dab08fa Package: AnnotationDbi Version: 1.66.0 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: 6c4b80075a9a9f5c4e3944f0532c62ac Package: AnnotationFilter Version: 1.28.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 2d2e19b72fb4ec4a0d3659e192d915fe Package: AnnotationForge Version: 1.46.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: ad1453a6171fc1c5a7f2b77b3fc79037 Package: AnnotationHub Version: 3.12.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 424403183ce1871be76215a81961a2f5 Package: AnnotationHubData Version: 1.34.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 8bebcd9a6d70e3fe14625500d7cbcead Package: annotationTools Version: 1.78.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: 151b352896b07e131704de246a06bce3 Package: annotatr Version: 1.30.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.23.10), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: fab1aa598ee6b48a6e315add1d429508 Package: anota Version: 1.52.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 721c088195f7d5dea5abf15c415c7b0a Package: anota2seq Version: 1.26.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: d8711e6e89f2f1fa2b10b7b64775fa0e Package: antiProfiles Version: 1.44.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: 913804e27f5d9addfa3888fb202d7c48 Package: AnVIL Version: 1.16.1 Depends: R (>= 3.6), dplyr Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocManager, BiocBaseUtils Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools License: Artistic-2.0 MD5sum: e85fe3b1c07a9906620953e3f345656d Package: AnVILBilling Version: 1.14.0 Depends: R (>= 4.1) Imports: methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 06e43319989d4b314bce558357e039bc Package: AnVILPublish Version: 1.14.0 Imports: AnVIL, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 59687a91f22a499d23454699d102f635 Package: AnVILWorkflow Version: 1.4.0 Depends: R (>= 4.2.0), Imports: utils, AnVIL, httr, methods, jsonlite, dplyr, tibble Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 691a025a9e70448f8003948f1d6b5d92 Package: APAlyzer Version: 1.18.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, HybridMTest Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset License: LGPL-3 MD5sum: 396520c3456fba10f01bc0fcff3659c5 Package: apComplex Version: 2.70.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 179211bb5464957352d9ae336f4101f0 Package: apeglm Version: 1.26.1 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 6c590feac988437d2208e2d14843c8cb Package: APL Version: 1.8.0 Depends: R (>= 4.2) Imports: reticulate, ggrepel, ggplot2, viridisLite, plotly, Seurat, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang, Matrix Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat License: GPL (>= 3) MD5sum: 45b5bf4839ee075e189bb70dd3324708 Package: appreci8R Version: 1.22.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db, utils License: LGPL-3 MD5sum: 81689a95f8b3227e4d4bc7e62332ad3a Package: aroma.light Version: 3.34.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: 69a7423f50db4a216ea715c96d430cd8 Package: ArrayExpress Version: 1.64.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: oligo, limma, httr, utils, jsonlite, rlang, tools, methods Suggests: affy License: Artistic-2.0 MD5sum: ae403086803bbee0caa1eb41e5a0aec7 Package: arrayMvout Version: 1.62.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy Imports: mdqc, affyContam, lumi Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: fcd5bdb65099f2c67b4cb8a0f85afebe Package: arrayQuality Version: 1.82.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 37f117fd1e61bf9d1681c4b30ae04461 Package: arrayQualityMetrics Version: 3.60.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 1d1fb380a6762ca05a6d68763ab9a4ff Package: ARRmNormalization Version: 1.44.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: 62ff6f992be9f9fdce5af2db30c10495 Package: artMS Version: 1.22.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, bit64, circlize, cluster, corrplot, data.table, dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: 8ac96b152418b1592df2305f3dbfeb9d Package: ASAFE Version: 1.30.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 8b7b327ac749a856583c91504c9f1064 Package: ASEB Version: 1.48.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: dfdfc0250ac69154d47b4f097d461bc5 Package: ASGSCA Version: 1.38.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 124840ff3f71d10a49059a0400dfbf36 Package: ASICS Version: 2.20.1 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: cddc3590cee4e124e5c224a079c8a8c3 Package: ASpli Version: 2.14.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply, txdbmaker License: GPL MD5sum: 3ad03f98eaa997010fff6a41fc65295f Package: AssessORF Version: 1.22.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 MD5sum: d4f40fe3ebbba1fa567af802999b49c3 Package: ASSET Version: 2.22.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 3d5ea57c49e5a85da85bb7fef71b9127 Package: ASSIGN Version: 1.40.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 289ac45cfa90253c78184a9cf33d2c0f Package: ASURAT Version: 1.8.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 8acdb9676919a722a931d4ad4a046ee0 Package: ATACseqQC Version: 1.28.0 Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: 7adfec5dae2a11f2931315c7c270b72e Package: atena Version: 1.10.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: 8f1df84593fa6c8cc4fe58d9664410be Package: atSNP Version: 1.20.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 213878336abe1bd55657f2ba6c5363f9 Package: attract Version: 1.56.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: dc2a71e39c7e3c81d9eec51f83b70efb Package: AUCell Version: 1.26.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: e0d0aa8186a56362d941cb1d3a020893 Package: autonomics Version: 1.12.1 Depends: R (>= 4.0) Imports: abind, BiocFileCache, BiocGenerics, bit64, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, BiocManager, BiocStyle, Biostrings, diagram, DBI, ensembldb, fpc, GenomicDataCommons, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, survival, survminer, testthat, UniProt.ws, writexl, XML License: GPL-3 MD5sum: b0fa77c17006b28206c65feb6c3ed677 Package: AWFisher Version: 1.18.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: 0183f063c6c7271f3bbb338a3a2aa8dd Package: awst Version: 1.12.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: d626bc55b5ee89e3a2dbf88ab6ad3b9a Package: BaalChIP Version: 1.30.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: c78cb428894542adb17b8a6e2283df01 Package: bacon Version: 1.32.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: dcd364a91b014c8ed1259786fb4f9618 Package: BADER Version: 1.42.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 89a33120fe337152e816f387f53e3947 Package: BadRegionFinder Version: 1.32.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: f8afc4c24ef409de249c405e77c05957 Package: BAGS Version: 2.44.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: e0c406ecaaea5a64d5b151f9730d1cb6 Package: ballgown Version: 2.36.0 Depends: R (>= 3.5.0), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), GenomeInfoDb Suggests: testthat, knitr, markdown License: Artistic-2.0 MD5sum: 3831117929cad6c1e2d7033c08ba2ae8 Package: bambu Version: 3.6.0 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 339928ae4596c32a9519a84796de2fe7 Package: bamsignals Version: 1.36.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: eae7eb3e1803b74b197ff2df445ab723 Package: BANDITS Version: 1.20.0 Depends: R (>= 4.3.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 6f4f12714bc23f9fa1356c4c5c865115 Package: bandle Version: 1.8.0 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang LinkingTo: Rcpp, RcppArmadillo, BH Suggests: coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: 2a744b63088afddf9dacfdb79e68922a Package: Banksy Version: 1.0.0 Depends: R (>= 4.4.0) Imports: aricode, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, matrixStats, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle License: file LICENSE MD5sum: fb5101cfda9a2539e7aea2392f98ddd9 Package: banocc Version: 1.28.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 31b637740215bbcef8b20dbc5f4998da Package: barcodetrackR Version: 1.12.0 Depends: R (>= 4.1) Imports: cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges, graphics, grDevices, magrittr, plyr, proxy, RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils Suggests: BiocStyle, knitr, magick, rmarkdown, testthat License: file LICENSE MD5sum: 222b0920764b85671ee4f21c3c4bcac1 Package: basecallQC Version: 1.28.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: 65b3c0e124161a3c2cb0ff566fc3dbe6 Package: BaseSpaceR Version: 1.48.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 60b56116a9b801a9e29cf10ccffeb9a5 Package: Basic4Cseq Version: 1.40.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: bcdd1b05fc9c6badc7f747aa34998c34 Package: BASiCS Version: 2.16.0 Depends: R (>= 4.2), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, posterior, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick License: GPL-3 MD5sum: 18ce83c0f8f1bab6788ea54388f9bf5c Package: BASiCStan Version: 1.6.0 Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1) Imports: methods, glmGamPoi, scran, scuttle, stats, utils, SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1) LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 MD5sum: a8efe95aee04618355a514a489e56781 Package: BasicSTARRseq Version: 1.32.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 MD5sum: c71648a850b77d5321528fc6902257ef Package: basilisk Version: 1.16.0 Depends: reticulate Imports: utils, methods, parallel, dir.expiry, basilisk.utils (>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: 4a7709c40ad69f6cef241298e0137753 Package: basilisk.utils Version: 1.16.0 Imports: utils, methods, tools, dir.expiry Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk License: GPL-3 MD5sum: a01d8ca99452dc93d84b0b9823603446 Package: batchelor Version: 1.20.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, DelayedArray, DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: b03bc2988ea385c8eddcc009d0292afc Package: BatchQC Version: 2.0.0 Depends: R (>= 4.3.0) Imports: data.table, DESeq2, dplyr, EBSeq, ggdendro, ggnewscale, ggplot2, limma, matrixStats, pheatmap, RColorBrewer, reader, reshape2, scran, shiny, stats, SummarizedExperiment, sva, tibble, tidyr, tidyverse, utils Suggests: BiocManager, BiocStyle, bladderbatch, dendextend, devtools, knitr, lintr, plotly, rmarkdown, shinythemes, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 2339c51f8c91d60fb63c90cdd386ea78 Package: BayesKnockdown Version: 1.30.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: d2bf0f8c296f8b2affc0796235cf6252 Package: BayesSpace Version: 1.14.0 Depends: R (>= 4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, assertthat, mclust, RCurl, DirichletReg, xgboost, utils, ggplot2, scales, BiocFileCache, BiocSingular LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: a53f8f765da9049b7f37e25fe085af03 Package: bayNorm Version: 1.22.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 3d7c765dc194ba122dcef6d7da8a3c0b Package: baySeq Version: 2.38.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 9a438e06aeb95c64b463746463824627 Package: BBCAnalyzer Version: 1.34.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: b80e17e9b06eb5c7d859b1ebb85c9f5e Package: BCRANK Version: 1.66.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: 839071b403ae21e552a707eb7c1db5f9 Package: bcSeq Version: 1.26.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: 7cea2799257364b67482a748d35caa18 Package: BDMMAcorrect Version: 1.22.0 Depends: R (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment Imports: Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats LinkingTo: Rcpp, RcppArmadillo, RcppEigen Suggests: knitr, rmarkdown, BiocGenerics License: GPL (>= 2) MD5sum: 2719197de94a03a32ece147b764dc12e Package: beachmat Version: 2.20.0 Imports: methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array License: GPL-3 MD5sum: 5841336254df9cfe173629192eb4c524 Package: beachmat.hdf5 Version: 1.2.0 Imports: methods, beachmat, HDF5Array, DelayedArray, Rcpp LinkingTo: Rcpp, beachmat, Rhdf5lib Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix License: GPL-3 MD5sum: 4441f55e732604036edafadbfddf5b41 Package: beadarray Version: 2.54.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE MD5sum: 4f306ca6d697d019cfe5eb8aba7686a4 Package: BeadDataPackR Version: 1.56.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 MD5sum: b0e59fa1221f93717e91796cfd8e4a93 Package: BEARscc Version: 1.24.0 Depends: R (>= 3.5.0) Imports: ggplot2, SingleCellExperiment, data.table, stats, utils, graphics, compiler Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF License: GPL-3 MD5sum: c6649e13edaacd4a01ecb62d793a2b07 Package: BEAT Version: 1.42.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: c7b1c07e2a6db675613f57a5b9ac6159 Package: BEclear Version: 2.20.0 Depends: BiocParallel (>= 1.14.2) Imports: futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave License: GPL-3 MD5sum: 10c31205fbb54b532aef7987bbccf9af Package: beer Version: 1.8.0 Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE MD5sum: 0c8fc863b6abda37c5d3c37ae1198428 Package: benchdamic Version: 1.10.0 Depends: R (>= 4.3.0) Imports: stats, stats4, utils, methods, phyloseq, TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR, DESeq2, limma, ALDEx2, corncob, SummarizedExperiment, MAST, Seurat, ANCOMBC, mixOmics, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, GUniFrac, metagenomeSeq, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, grDevices, tidytext Suggests: knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat License: Artistic-2.0 MD5sum: 179df7d9093afc933cdb5ac68720d513 Package: BERT Version: 1.0.0 Depends: R (>= 4.3.0) Imports: cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators (>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>= 0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: c1143c4dbd8bf47a5cb90915ba2e97cc Package: betaHMM Version: 1.0.0 Depends: R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges Imports: stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 2104c9beb41e5c48630e48157d07e466 Package: bettr Version: 1.0.0 Depends: R (>= 4.4.0) Imports: dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6), tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid, methods, cowplot, Hmisc, sortable, shinyjqui, grDevices, scales, DT, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 0c784d0efabfc62f0ccb29a16814086f Package: BG2 Version: 1.4.0 Depends: R (>= 4.2.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), MASS (>= 7.3-58.1), stats (>= 4.2.2) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: fb96db653d1aee9f7b79fc33f8388760 Package: BgeeCall Version: 1.20.0 Depends: R (>= 3.6) Imports: GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5 Suggests: knitr, testthat, rmarkdown, AnnotationHub, httr License: GPL-3 + file LICENSE MD5sum: 314d64cdbe50b0bd227f015c99253611 Package: BgeeDB Version: 2.30.0 Depends: R (>= 3.6.0), topGO, tidyr Imports: R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: f998e282fa929d85993039ab6b2e6dbe Package: bgx Version: 1.70.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Imports: Rcpp (>= 0.11.0) LinkingTo: Rcpp Suggests: affydata, hgu95av2cdf License: GPL-2 MD5sum: ca59005c546722d056f34e8c71d111ee Package: BicARE Version: 1.62.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db Imports: methods Suggests: hgu95av2 License: GPL-2 MD5sum: 548258dd1794a63133ce546a9aabb345 Package: BiFET Version: 1.24.0 Depends: R (>= 3.5.0) Imports: stats, poibin, GenomicRanges Suggests: rmarkdown, testthat, knitr License: GPL-3 MD5sum: 6b2a1ea512e8b0975ef6480cb6115313 Package: bigmelon Version: 1.30.0 Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4), methods, minfi (>= 1.21.0), Biobase, methylumi Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 MD5sum: c93422cf3c7347387dd6459832890c43 Package: BindingSiteFinder Version: 2.2.0 Depends: GenomicRanges, R (>= 4.2) Imports: tidyr, tibble, plyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap, RColorBrewer, lifecycle, rlang, forcats, dplyr, GenomicFeatures, IRanges, kableExtra, ggdist Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr License: Artistic-2.0 MD5sum: e933ff3304ea07c44803dd6e75d19f51 Package: Biobase Version: 2.64.0 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma License: Artistic-2.0 MD5sum: 1ce2bcd4f6826b502e2df848ee1e36e3 Package: biobroom Version: 1.36.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment License: LGPL MD5sum: 93753fc40e34190a81cf9e2abbc14c1c Package: bioCancer Version: 1.32.0 Depends: R (>= 3.6.0), radiant.data (>= 0.9.1), cBioPortalData, XML(>= 3.98) Imports: R.oo, R.methodsS3, DT (>= 0.3), dplyr (>= 0.7.2), tidyr, shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods, AnnotationDbi, shinythemes, Biobase, geNetClassifier, org.Hs.eg.db, org.Bt.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(<= 1.01), visNetwork, htmlwidgets, plyr, tibble, GO.db Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) License: AGPL-3 | file LICENSE MD5sum: d5f111e2ec33bfe61a533e4bbed995de Package: BioCartaImage Version: 1.2.0 Depends: R (>= 4.3.0) Imports: magick, grid, stats, grDevices, utils Suggests: testthat, knitr, BiocStyle, ragg License: MIT + file LICENSE MD5sum: fbc585e975793f7007957f2d69ce82c2 Package: BiocBaseUtils Version: 1.6.0 Depends: R (>= 4.2.0) Imports: methods, utils Suggests: knitr, rmarkdown, BiocStyle, tinytest License: Artistic-2.0 MD5sum: 048acb5705b14b939a2e14123665c494 Package: BiocBook Version: 1.2.0 Depends: R (>= 4.3) Imports: BiocGenerics, available, cli, glue, gert, gh, gitcreds, httr, usethis, dplyr, purrr, tibble, methods, rprojroot, stringr, yaml, tools, utils, rlang, quarto, renv Suggests: BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown License: MIT + file LICENSE MD5sum: 508411a862cd92435172335d4469c419 Package: BiocCheck Version: 1.40.0 Depends: R (>= 4.3.0) Imports: BiocBaseUtils, BiocFileCache, BiocManager, biocViews (>= 1.33.7), callr, codetools, graph, httr2, knitr, methods, rvest, stringdist, tools, utils Suggests: RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown, downloader, devtools (>= 1.4.1), usethis, BiocStyle, GenomicRanges, gert License: Artistic-2.0 MD5sum: 56f75671fff9607ab7323bc7b793713b Package: BiocFHIR Version: 1.6.0 Depends: R (>= 4.2) Imports: DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils, methods, BiocBaseUtils Suggests: knitr, testthat, rjsoncons, igraph, BiocStyle License: Artistic-2.0 MD5sum: a3236b4cc2bdd576ea7aec2dc3161cfe Package: BiocFileCache Version: 2.12.0 Depends: R (>= 3.4.0), dbplyr (>= 1.0.0) Imports: methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl, httr Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer License: Artistic-2.0 MD5sum: 43634531f602565774a0c885049b2cef Package: BiocGenerics Version: 0.50.0 Depends: R (>= 4.0.0), methods, utils, graphics, stats Imports: methods, utils, graphics, stats Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit License: Artistic-2.0 MD5sum: 67c50ea05095591f54662f8a7e3c1912 Package: biocGraph Version: 1.66.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 MD5sum: 009e2bb3b9913e29eecabf5f5b9dbd19 Package: BiocHubsShiny Version: 1.4.0 Depends: R (>= 4.3.0), shiny Imports: AnnotationHub, ExperimentHub, DT, htmlwidgets, S4Vectors, shinyAce, shinyjs, shinythemes, shinytoastr, utils Suggests: BiocManager, BiocStyle, knitr, rmarkdown, sessioninfo, shinytest2 License: Artistic-2.0 MD5sum: 43764fb6524104780a77bc038e9504fa Package: BiocIO Version: 1.14.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, S4Vectors, methods, tools Suggests: testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: e2c674db82b50dc296863d15abca36fd Package: BiocNeighbors Version: 1.22.0 Imports: Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix LinkingTo: Rcpp, RcppHNSW Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW License: GPL-3 MD5sum: c50f707306493a82be43dc80eec824a1 Package: BiocOncoTK Version: 1.24.0 Depends: R (>= 3.6.0), methods, utils Imports: ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr, rjson, dplyr, magrittr, grid, DT, GenomicRanges, IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures, curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz, MASS, grDevices Suggests: knitr, dbplyr, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75, rmarkdown, rhdf5client, AnnotationHub License: Artistic-2.0 MD5sum: 43276265b0be18d035df8049447967fe Package: BioCor Version: 1.28.0 Depends: R (>= 3.4.0) Imports: BiocParallel, GSEABase, Matrix, methods Suggests: airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat (>= 3.0.0), WGCNA License: MIT + file LICENSE MD5sum: f0bd93c9a7f1a3a56b3692a32eaa7af5 Package: BiocParallel Version: 1.38.0 Depends: methods, R (>= 3.5.0) Imports: stats, utils, futile.logger, parallel, snow, codetools LinkingTo: BH, cpp11 Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table Enhances: Rmpi License: GPL-2 | GPL-3 MD5sum: 00958fa4fcf98290766b1851ba1934d5 Package: BiocPkgTools Version: 1.22.0 Depends: htmlwidgets Imports: BiocFileCache, BiocManager, biocViews, tibble, magrittr, methods, rlang, stringr, stats, rvest, dplyr, xml2, readr, httr, htmltools, DT, tools, utils, igraph, jsonlite, gh, RBGL, graph, rorcid Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, networkD3, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment License: MIT + file LICENSE MD5sum: 5fb3501e1578cafb9e4a74cd9620230c Package: biocroxytest Version: 1.0.0 Depends: R (>= 4.4.0) Imports: cli, glue, roxygen2, stringr Suggests: BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 29edf07df2d46dad8de556186ffb3c43 Package: BiocSet Version: 1.18.0 Depends: R (>= 3.6), dplyr Imports: methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO, AnnotationDbi, KEGGREST, ontologyIndex, tidyr Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: c14e01e9b61a1f4dbd26dc60e8949c41 Package: BiocSingular Version: 1.20.0 Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat LinkingTo: Rcpp, beachmat Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix License: GPL-3 MD5sum: 2d45b798bea39e9c29d38e6be8995277 Package: BiocSklearn Version: 1.26.0 Depends: R (>= 4.0), reticulate, methods, SummarizedExperiment Imports: basilisk Suggests: testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown, knitr License: Artistic-2.0 MD5sum: 17b4f4147011ecdfaaee4c254d2aad75 Package: BiocStyle Version: 2.32.1 Imports: bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager Suggests: BiocGenerics, RUnit, htmltools License: Artistic-2.0 MD5sum: 8a42961d2fc84edb1ff2f9c86cfbe568 Package: biocthis Version: 1.14.0 Imports: BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1) Suggests: BiocStyle, covr, devtools, knitr, pkgdown, RefManageR, rmarkdown, sessioninfo, testthat, utils License: Artistic-2.0 MD5sum: 0854dd71710fe668a004220e492b4528 Package: BiocVersion Version: 3.19.1 Depends: R (>= 4.4.0) License: Artistic-2.0 MD5sum: d938442f83d71cc9ae653ecca7e54b6f Package: biocViews Version: 1.72.0 Depends: R (>= 3.6.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, BiocManager Suggests: BiocGenerics, knitr, commonmark, BiocStyle License: Artistic-2.0 MD5sum: 5bc5bb1a355ca69c5602115185cab268 Package: BiocWorkflowTools Version: 1.30.0 Depends: R (>= 3.4) Imports: BiocStyle, bookdown, git2r, httr, knitr, rmarkdown, rstudioapi, stringr, tools, utils, usethis License: MIT + file LICENSE MD5sum: 86db6930aa99e6dc063cd9ee861ef4b4 Package: biodb Version: 1.12.0 Depends: R (>= 4.1.0) Imports: BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, git2r, jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, stats, stringr, tools, withr, yaml LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2 License: AGPL-3 MD5sum: 983121de21dc12e0fb35fb8a132e492f Package: biodbChebi Version: 1.10.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.1.5) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr License: AGPL-3 MD5sum: 727beb83a460324f02d4bde55f4a1693 Package: biodbExpasy Version: 1.8.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.1), R6, stringr, chk Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 8ef54af7e58c96ee912d9372e1407a7c Package: biodbHmdb Version: 1.10.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.3.2), Rcpp, zip LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 911a6ab6b42acc54a14eba104ec28dc8 Package: biodbKegg Version: 1.10.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.4.2), chk, lifecycle Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, igraph, magick, lgr License: AGPL-3 MD5sum: 0f467ca1b8baa350456aa4d9a285cbbe Package: biodbNcbi Version: 1.8.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.2), R6, XML, chk Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: edb46400fd1ed79e72556ab7ce60eb3a Package: biodbNci Version: 1.8.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.1), R6, Rcpp, chk LinkingTo: Rcpp, testthat Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: c5aaeacaae875a980ad6a228a33fc740 Package: biodbUniprot Version: 1.10.0 Depends: R (>= 4.1.0) Imports: R6, biodb (>= 1.4.2) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr, covr License: AGPL-3 MD5sum: 84d3b1d05c550c9f645a091bf64e12cc Package: bioDist Version: 1.76.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 MD5sum: d19a94ca21305a5979771071f0729b3a Package: biomaRt Version: 2.60.1 Depends: methods Imports: utils, AnnotationDbi, progress, stringr, httr2, digest, BiocFileCache, rappdirs, xml2 Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, httptest2 License: Artistic-2.0 MD5sum: b5be92ef37f9d0277a382ef439a57e5d Package: biomformat Version: 1.32.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 MD5sum: 623aace1ed7189f45a8eeea58881d1b6 Package: BioMVCClass Version: 1.72.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL MD5sum: a1fb67d585dc4609055136bc02b8da7e Package: biomvRCNS Version: 1.44.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 16fcbfee5b6b83490006561cb4176817 Package: BioNAR Version: 1.6.0 Depends: R (>= 3.5.0), igraph (>= 2.0.1.1), poweRlaw, latex2exp, RSpectra, Rdpack Imports: stringr, viridis, clusterCons, fgsea, grid, methods, AnnotationDbi, dplyr, GO.db, org.Hs.eg.db (>= 3.19.1), rSpectral, WGCNA, ggplot2, ggrepel, minpack.lm, cowplot, data.table, scales, stats, Matrix Suggests: knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR License: Artistic-2.0 MD5sum: 1d9cd87093e0aeb7a269495671dfd528 Package: BioNERO Version: 1.12.0 Depends: R (>= 4.1) Imports: WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva, RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel, patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep, stats, grDevices, utils, methods, BiocParallel, minet, GENIE3, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr License: GPL-3 MD5sum: 75304316eadc7f2ded39f63b2310bb06 Package: BioNet Version: 1.64.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) MD5sum: e5d1177b04f91c9635c61267fbbaac51 Package: BioQC Version: 1.32.0 Depends: R (>= 3.5.0), Biobase Imports: edgeR, Rcpp, methods, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer License: GPL (>= 3) + file LICENSE MD5sum: 0b86b4f64eb23c369c898268e942fc91 Package: Biostrings Version: 2.72.1 Depends: R (>= 4.0.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), XVector (>= 0.37.1), GenomeInfoDb Imports: methods, utils, grDevices, stats, crayon LinkingTo: S4Vectors, IRanges, XVector Suggests: graphics, pwalign, 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 (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 856b99f5a60415d64c829a9d073c6fa7 Package: BioTIP Version: 1.18.0 Depends: R (>= 3.6) Imports: igraph, cluster, psych, stringr, GenomicRanges, MASS, scran Suggests: knitr, markdown, base, rmarkdown, ggplot2 License: GPL-2 MD5sum: f98821cb9ecd1fe456d767033a5f1485 Package: biotmle Version: 1.28.0 Depends: R (>= 4.0) Imports: stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: MIT + file LICENSE MD5sum: b7b29b92b4ea1112020e2672ebba5580 Package: biovizBase Version: 1.52.0 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: 5909e92189e22169351ffe15c7ee49e9 Package: BiRewire Version: 3.36.0 Depends: igraph, slam, Rtsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: bd0f75e079c0b9771208e3d7baa8b75f Package: biscuiteer Version: 1.18.0 Depends: R (>= 4.1.0), biscuiteerData, bsseq Imports: readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, IRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel Suggests: DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle License: GPL-3 MD5sum: 80c02fe2413d8eeba729dd9bb0cb6a0f Package: BiSeq Version: 1.44.0 Depends: R (>= 3.5.0), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 MD5sum: 46d03191d088c99bcbf824a54a3e1f46 Package: blacksheepr Version: 1.18.0 Depends: R (>= 3.6) Imports: grid, stats, grDevices, utils, circlize, viridis, RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl License: MIT + file LICENSE MD5sum: ac63988e4f7041a9fc6d09f8118d720f Package: blima Version: 1.38.0 Depends: R(>= 3.3) Imports: beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics LinkingTo: Rcpp Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr License: GPL-3 MD5sum: b8fa04fe3f050ea29edd6151ba2c1263 Package: BLMA Version: 1.28.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase, metafor, methods Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: e7c791d5f7ff0d9ef2db592b32d883d0 Package: BloodGen3Module Version: 1.12.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, ExperimentHub, methods, grid, graphics, stats, grDevices, circlize, testthat, ComplexHeatmap(>= 1.99.8), ggplot2, matrixStats, gtools, reshape2, preprocessCore, randomcoloR, V8, limma Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown License: GPL-2 MD5sum: 03de1c3025bdad32062bf3abb21ae33b Package: bluster Version: 1.14.0 Imports: stats, methods, utils, cluster, Matrix, Rcpp, igraph, S4Vectors, BiocParallel, BiocNeighbors LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster License: GPL-3 MD5sum: 2235219aba6f48630c274cfc4ed5c7a1 Package: bnbc Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils, HiCBricks LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: e05304a4084cc9c46d85ff390f88a904 Package: bnem Version: 1.12.0 Depends: R (>= 4.1) Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit License: GPL-3 MD5sum: ca413087c76f85e6a9a6c99dde67955f Package: BOBaFIT Version: 1.8.0 Depends: R (>= 2.10) Imports: dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat License: GPL (>= 3) MD5sum: e11463fed0081f40effdce65594a8186 Package: borealis Version: 1.8.0 Depends: R (>= 4.2.0), Biobase Imports: doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist, bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot, dplyr, rlang, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL-3 MD5sum: e7f6d934b7bf94bb9dce2b50fa76c424 Package: BPRMeth Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 6e76a113180fc0bfe138a1cb3a913788 Package: BRAIN Version: 1.50.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: 9fb565062fcd6c1861c78fbc06892a1d Package: branchpointer Version: 1.30.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: 59be190305d0a94a353262c0c9e551d9 Package: breakpointR Version: 1.22.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: 230663309fda0c7a871c7ff6d09b3570 Package: brendaDb Version: 1.18.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: 8f374d387f2863238743548fde7099c7 Package: BREW3R.r Version: 1.0.1 Imports: GenomicRanges, methods, rlang, S4Vectors, utils Suggests: testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle, rtracklayer License: GPL-3 MD5sum: 13b92ea4b586629fa103bf3a5848e0ae Package: BridgeDbR Version: 2.14.0 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: 72f53b90b9311df8c731be07649eeb60 Package: BrowserViz Version: 2.26.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 28bfc4015f257d46bb59c3b1ce09ff8e Package: BSgenome Version: 1.72.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.25.6), GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), BiocIO, rtracklayer Imports: utils, stats, matrixStats, XVector, Rsamtools Suggests: BiocManager, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge License: Artistic-2.0 MD5sum: 8ad1c201e86ecd8220b63efb11583dbc Package: BSgenomeForge Version: 1.4.0 Depends: R (>= 4.3.0), methods, BiocGenerics, IRanges, GenomeInfoDb (>= 1.33.17), Biostrings, BSgenome Imports: utils, stats, Biobase, S4Vectors, GenomicRanges, BiocIO, rtracklayer Suggests: GenomicFeatures, Rsamtools, testthat, knitr, rmarkdown, BiocStyle, devtools, BSgenome.Celegans.UCSC.ce2 License: Artistic-2.0 MD5sum: 53bcc409283cee86df2cba4b4555957d Package: bsseq Version: 1.40.0 Depends: R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5) Imports: IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), batchtools License: Artistic-2.0 MD5sum: 0a18d2c65508314e6fe516eb097b7487 Package: BubbleTree Version: 2.34.0 Depends: R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr Imports: BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: f04e28ebf48b743a83fc5575d2f2425a Package: BufferedMatrix Version: 1.68.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: 722d392a9fbfedbe4959c742d87092c3 Package: BufferedMatrixMethods Version: 1.68.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) MD5sum: 8403e726b8bdb34464e380b0963c0eda Package: bugsigdbr Version: 1.10.0 Depends: R (>= 4.1) Imports: BiocFileCache, methods, vroom, utils Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: ab919276173486772618edfb151c0f72 Package: BUMHMM Version: 1.28.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: 96375bb3be2ff94e25d7a6b9c06c9b51 Package: bumphunter Version: 1.46.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 9724ebd271023f5ce6d045c19d738a8e Package: BumpyMatrix Version: 1.12.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 5c85519b78d78c4ce2ad09730611d517 Package: BUS Version: 1.60.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: 252a5860b8e9c29b03ea04ef6d79d8f2 Package: BUScorrect Version: 1.22.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 29c5998088264ea3e6244faa40c9a07e Package: BUSpaRse Version: 1.18.0 Depends: R (>= 3.6) Imports: AnnotationDbi, AnnotationFilter, biomaRt, BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH Suggests: knitr, rmarkdown, testthat, BiocStyle, txdbmaker, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: 9185484ec78ef4f9ee62cb96bca203f6 Package: BUSseq Version: 1.10.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: 13333565023bc07c3ca407ab944cb97c Package: CaDrA Version: 1.2.0 Depends: R (>= 4.3.0) Imports: doParallel, ggplot2, gplots, graphics, grid, gtable, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) License: GPL-3 + file LICENSE MD5sum: 12f11da507920eb6b11f2791c2945b86 Package: CAEN Version: 1.12.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle License: GPL-2 MD5sum: 0dfb411069f5754ca1bec0e9b3da7f5f Package: CAFE Version: 1.40.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 522e33cc408f0c81a66cdc8cd3ac9cbb Package: CAGEfightR Version: 1.24.0 Depends: R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>= 1.38.2), SummarizedExperiment (>= 1.8.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3), Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), GenomicAlignments(>= 1.22.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE MD5sum: 52f2088d81b8b85e1d4b085a579386c9 Package: cageminer Version: 1.10.0 Depends: R (>= 4.1) Imports: ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: 3e7603ef224c24d0787969cfb49a9ad1 Package: CAGEr Version: 2.10.0 Depends: methods, MultiAssayExperiment, R (>= 4.1.0) Imports: BiocGenerics, BiocParallel, BSgenome, CAGEfightR, data.table, DelayedArray, DelayedMatrixStats, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr, Rsamtools, reshape2, rtracklayer, S4Vectors (>= 0.27.5), som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: b203e923cfa849ade3d307dcc01eb6c1 Package: calm Version: 1.18.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 0120547e5826e69e8489af976552d447 Package: CaMutQC Version: 1.0.0 Depends: R (>= 4.0.0) Imports: ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 3af1ab0da2ff77c204023f83b745b899 Package: canceR Version: 1.38.0 Depends: R (>= 4.3), tcltk, cBioPortalData Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr, graphics, stats, utils, grDevices, R.oo, R.methodsS3 Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: c146fa6c61d1ca72b8b7ecfa352fd5aa Package: cancerclass Version: 1.48.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: c00d3202eabe5bb28a0a25af04387cca Package: CancerSubtypes Version: 1.30.0 Depends: R (>= 4.0), sigclust, NMF Imports: cluster, impute, limma, ConsensusClusterPlus, grDevices, survival Suggests: BiocGenerics, knitr, RTCGA.mRNA, rmarkdown License: GPL (>= 2) MD5sum: 1ef03c3da8c98dd3d144b50d60b6cc82 Package: cardelino Version: 1.6.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 MD5sum: 1fcd7d36b090e36cbb761ac6ed357ebf Package: Cardinal Version: 3.6.3 Depends: R (>= 4.3), ProtGenerics, BiocGenerics, BiocParallel, S4Vectors (>= 0.27.3), methods, stats, stats4 Imports: CardinalIO, Biobase, EBImage, graphics, grDevices, irlba, Matrix, matter (>= 2.6.2), nlme, parallel, utils Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: d76cf032c267a5ad9d4d135502f22d78 Package: CardinalIO Version: 1.2.1 Depends: R (>= 4.3), matter, ontologyIndex Imports: methods, S4Vectors, stats, utils, tools Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 871bdc6d8a1349329a3e20595054c3a8 Package: CARNIVAL Version: 2.14.0 Depends: R (>= 4.0) Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo License: GPL-3 MD5sum: 134e05038e21a17143da9b906f2289c2 Package: Category Version: 2.70.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 3723c4db2ad01438c48c57b94e46cd80 Package: categoryCompare Version: 1.48.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown License: GPL-2 MD5sum: e9660e02697c0ee8febbbaa217028309 Package: CausalR Version: 1.36.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 833187364b0d46a19ddedaf1859c5516 Package: cbaf Version: 1.26.3 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4c8586e719e9614b261a3dc496db0318 Package: CBEA Version: 1.4.0 Depends: R (>= 4.2.0) Imports: BiocParallel, BiocSet, dplyr, lmom, fitdistrplus, magrittr, methods, mixtools, Rcpp (>= 1.0.7), stats, SummarizedExperiment, tibble, TreeSummarizedExperiment, tidyr, glue, generics, rlang, goftest LinkingTo: Rcpp Suggests: phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia, purrr License: MIT + file LICENSE MD5sum: f0ef15d631af7874522d9c9826de661c Package: cBioPortalData Version: 2.16.0 Depends: R (>= 4.2.0), AnVIL (>= 1.7.1), MultiAssayExperiment Imports: BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 MD5sum: d475026dcb29fb2821b52c96a75e12e1 Package: CBNplot Version: 1.4.0 Depends: R (>= 4.3.0) Imports: ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang, oaqc Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, DESeq2, GEOquery, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 74b866e3dd645558f64d764df72cf58b Package: cbpManager Version: 1.12.0 Depends: shiny, shinydashboard Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 17019a7985aa164e7a997b26607d6e30 Package: ccImpute Version: 1.6.0 Imports: Rcpp, matrixStats, stats, SIMLR, BiocParallel LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, SingleCellExperiment, mclust, testthat (>= 3.0.0) License: GPL-3 MD5sum: 91d5f1825e7c66ba899f9c7003313f58 Package: ccmap Version: 1.30.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.30.4), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE MD5sum: fc701f6cd160de12cef0846463d2862b Package: CCPlotR Version: 1.2.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: e32601580d8db53b81af3c008755cace Package: CCPROMISE Version: 1.30.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 8eea5b71b92d8ef6d7dabe5da3bbb75d Package: ccrepe Version: 1.40.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit License: MIT + file LICENSE MD5sum: dc96d978d7f07819e7ba38ba2756fbcd Package: CDI Version: 1.2.0 Depends: R(>= 3.6) Imports: matrixStats, Seurat, SeuratObject, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle License: GPL-3 + file LICENSE MD5sum: ee31c5d11d50b6d37176a1f87ec3d31e Package: celaref Version: 1.22.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: e53f17ff9fa96f2a2ae0eefb199ecc7d Package: celda Version: 1.20.0 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 461cd7bfd1c54470dfccf9927b91214d Package: CellBarcode Version: 1.10.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, zlibbioc, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: 1dc03fe0656113af694368e37577fba0 Package: cellbaseR Version: 1.28.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: 2cb5a9fb5edd67f1954e454047e8be88 Package: CellBench Version: 1.20.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: 98105cd3ce9f911f6a916cb57ffae674 Package: cellHTS2 Version: 2.68.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: GSEABase, Category, stats4, BiocGenerics Suggests: ggplot2, GO.db License: Artistic-2.0 MD5sum: 842eda88fb1100b0d411345ec5152d32 Package: CelliD Version: 1.12.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: aa48dda097c727f7d47b2739f2f276ae Package: cellity Version: 1.32.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 3b4042d9e35fbf1c3fc80855934c6fde Package: CellMapper Version: 1.30.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: 5bd55b93b4ca43e8d2cdad4a7ce2e93f Package: cellmigRation Version: 1.12.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: 233e19c884e3626802af07a95ac59d39 Package: CellMixS Version: 1.20.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: 7d916db1e912fa228971c027ba1fe3cc Package: CellNOptR Version: 1.50.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: e230870a80131d031332e8689dae9a3c Package: cellscape Version: 1.28.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 14be5559040034e732b35dda04920953 Package: CellScore Version: 1.24.0 Depends: R (>= 4.3.0) Imports: Biobase (>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0), SummarizedExperiment Suggests: hgu133plus2CellScore, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1d3f9b4fecdc551fe012a65e7f28f3e4 Package: CellTrails Version: 1.22.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 3a529ef8b8531f5793df0fb6016e1e0b Package: cellxgenedp Version: 1.8.0 Depends: dplyr Imports: httr, curl, utils, tools, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 MD5sum: de70839673b430dcb4fbbceec2eb9c00 Package: CEMiTool Version: 1.28.0 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: 969c042f65b02da5ed05d261e5e7bbda Package: censcyt Version: 1.12.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: 6823932ccb42f3b92e4947510c7ebd05 Package: Cepo Version: 1.10.2 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr, purrr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap License: MIT + file LICENSE MD5sum: 57b25711c75c3581ac145405c7d7a768 Package: ceRNAnetsim Version: 1.16.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: 1df07d022402dd85dd7921f0428764b5 Package: CeTF Version: 1.16.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: e803957bd25000e42a0f967ee936abff Package: CexoR Version: 1.42.0 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: 04b53608f518a98b3de70d3a23ecc1c6 Package: CFAssay Version: 1.38.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: e2ba3d978e0796f76f9893193dc9999b Package: cfdnakit Version: 1.2.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang Suggests: rmarkdown, knitr, roxygen2, BiocStyle License: GPL-3 MD5sum: 0ddc766612fdefa40295969c06c2522e Package: cfDNAPro Version: 1.10.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38 Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: ccd1557030c5bc5192ffdcea45aa563c Package: cfTools Version: 1.4.0 Imports: Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData LinkingTo: Rcpp, BH Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: file LICENSE MD5sum: b7cd4930145a61926f8add407b65060f Package: CGEN Version: 3.40.0 Depends: R (>= 4.0), survival, mvtnorm Imports: stats, graphics, utils, grDevices Suggests: cluster License: GPL-2 + file LICENSE MD5sum: 9676386bb412650e67842ccb9c048c3c Package: CGHbase Version: 1.64.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: 6fe4c3f1e41fe0350228bed3704cc49d Package: CGHcall Version: 2.66.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: 8d2dad369bbfe96bd156fd35422f95c5 Package: cghMCR Version: 1.62.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 3f69f6133d0c20ab0cdd24fd14d08268 Package: CGHnormaliter Version: 1.58.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: b72e007375fbf08248c5a8247fe614b8 Package: CGHregions Version: 1.62.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase MD5sum: 451ddbdbe11905146e7bad58ffd83e2e Package: ChAMP Version: 2.34.0 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT, RPMM Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,kpmt,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: 3aaf19bfe004dbec8c85db7d57795d9f Package: ChemmineR Version: 3.56.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg,jsonlite,stringi LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex Enhances: ChemmineOB License: Artistic-2.0 MD5sum: 7db2309785299464f2bae3bc61d0690c Package: CHETAH Version: 1.20.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: cfb0029e321820bd5026b3fb06296c5c Package: Chicago Version: 1.32.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: b3860d2c9f8585983399cd9f4800db86 Package: chihaya Version: 1.4.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: 1113a115c80657143ff30cb55383d4b3 Package: chimeraviz Version: 1.30.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: 30fdcb1a118b475b4062112f3b33c698 Package: ChIPanalyser Version: 1.26.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 1bf8033524fad6cc1192fb264ca40583 Package: ChIPComp Version: 1.34.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,GenomeInfoDb,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: 3cd03dd5fc2e423a4a610a63afedb66d Package: chipenrich Version: 2.28.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: e24502eca54675f79d2df5a86985d2a0 Package: ChIPexoQual Version: 1.28.0 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: 5266a562b947f9503c3e8124b633de9d Package: ChIPpeakAnno Version: 3.38.1 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache License: GPL (>= 2) MD5sum: 4f5c65d93f0aa92e1df8c88b8097434d Package: ChIPQC Version: 1.40.0 Depends: R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19), BiocParallel Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) MD5sum: 0cf328a3b647d14c535f01009eed26c8 Package: ChIPseeker Version: 1.40.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, aplot, yulab.utils, tibble Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, prettydoc License: Artistic-2.0 MD5sum: bfec2518247350d39f8936b755555fe0 Package: chipseq Version: 1.54.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr License: Artistic-2.0 MD5sum: 1f381393e1d40301c999e019a9bb5c72 Package: ChIPseqR Version: 1.58.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: bd799e48f6f7fc1ed55fcbf2eca9db75 Package: ChIPsim Version: 1.58.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: 8c3f1fa8b5150f102c6282d220b17b79 Package: ChIPXpress Version: 1.48.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: add233a501ea489000d4e55cea717253 Package: chopsticks Version: 1.70.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: 4553f23d038a19816faeada8a556013d Package: chromDraw Version: 2.34.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: ddfce9ebf09c9f0fc5209a58d02f96d3 Package: ChromHeatMap Version: 1.58.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: cf52c21bce971de68eaa216b1a0c0bf1 Package: chromPlot Version: 1.32.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: f05739770e7f9cd06a43fc93d64938a0 Package: ChromSCape Version: 1.14.0 Depends: R (>= 4.1) Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr License: GPL-3 MD5sum: faa8ee0a540620d67aac2998e5af5e6d Package: chromstaR Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2, chromstaRData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm Suggests: knitr, BiocStyle, testthat, biomaRt License: Artistic-2.0 MD5sum: 5a6a27768bc362644a1a9135fcdaa5ea Package: cicero Version: 1.22.0 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: f587262b0b430c9dd0fbd0e63aaeb998 Package: CIMICE Version: 1.12.0 Imports: dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot License: Artistic-2.0 MD5sum: 134e7b641f66d0dac9ce014381dd788a Package: CINdex Version: 1.32.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, GenomeInfoDb,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils License: GPL (>= 2) MD5sum: aea37963b802ad18ead3337d626e6f89 Package: circRNAprofiler Version: 1.18.0 Depends: R(>= 4.3.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: 527b7a4e26998f950d425f8e1e94de99 Package: CircSeqAlignTk Version: 1.6.0 Depends: R (>= 4.2) Imports: stats, tools, utils, R.utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny, shinyFiles, shinyjs, plotly, parallel, htmltools Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 1056690c416caef55ede77634d7a692e Package: cisPath Version: 1.44.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) MD5sum: d2aa32927f6179a21fba2c7261be0d3c Package: CiteFuse Version: 1.16.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions LinkingTo: Rcpp Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: a38d59ef718d4862cd40d73cd8d30ba2 Package: ClassifyR Version: 3.8.2 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.0.0), ggpubr, reshape2, ggupset Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale License: GPL-3 MD5sum: 9b6e9ae078fdfe5b207e2dfe6ad5b21c Package: cleanUpdTSeq Version: 1.42.0 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 MD5sum: b623f2c2d82af25b21d8ce99287ef48f Package: cleaver Version: 1.42.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) MD5sum: 9830d9648e0c654fdfe7917a72c86dd4 Package: clevRvis Version: 1.4.0 Imports: shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl, dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets, colorspace, shinyhelper, shinycssloaders, ggnewscale, shinydashboard, DT, colourpicker, grDevices, methods, utils, stats, ggplot2, magrittr, tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 8cfe496ee5cc7f0bb1b8ca00e81543a5 Package: clippda Version: 1.54.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: d3a3dcfa4489eba608da74017893067f Package: clipper Version: 1.44.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: 05cc43eae8f8f9ac7e08028dc7b174f5 Package: cliProfiler Version: 1.10.0 Depends: S4Vectors, methods, R (>= 4.1) Imports: dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome, Biostrings, utils Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 2db7829dd888224d2db4b8f842c86b44 Package: Clomial Version: 1.40.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: 7edfa657e33c1287afe63ac61c689fe9 Package: clst Version: 1.52.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: b16861e4ce92b3ad25c0eca52e39a1d6 Package: clstutils Version: 1.52.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit License: GPL-3 MD5sum: d2145e264aaf603e24639600011aff93 Package: ClustAll Version: 1.0.0 Depends: R (>= 4.2.0) Imports: FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 MD5sum: 006c3f67632047f5367160f7ce0e494c Package: clustComp Version: 1.32.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: c57c9632fe2ba7ffe190b78cafd1d84d Package: clusterExperiment Version: 2.24.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: d1456b45f320a3a6ea66845a75855b2a Package: ClusterFoldSimilarity Version: 1.0.0 Imports: methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 MD5sum: c909f761289e5350969150759e2505f8 Package: ClusterJudge Version: 1.26.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: fcabeb9d15c939beb7b80dd4b5e6c5a1 Package: clusterProfiler Version: 4.12.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, downloader, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3), GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.0.7) Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat License: Artistic-2.0 MD5sum: b86d6d0e01a9dfe2314298ed2631684b Package: clusterSeq Version: 1.28.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 3e84a4b2bdc863cf89db450c0aea1a1c Package: ClusterSignificance Version: 1.32.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: 009add19cab4fcb65433c2c9c6313628 Package: clusterStab Version: 1.76.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: da0482cad7454952dbdc86aca82f6f6d Package: clustifyr Version: 1.16.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: 0e30705dd063d24ecdf0a20fff6bab5c Package: ClustIRR Version: 1.2.0 Depends: R (>= 4.3.0) Imports: stringdist, methods, stats, utils, igraph, visNetwork, blaster, pwalign, grDevices, parallel Suggests: BiocStyle, knitr, testthat, ggplot2, patchwork, ggrepel License: GPL-3 + file LICENSE MD5sum: 7a81e5d44d381ecdd727ef4f94c5aed6 Package: CMA Version: 1.62.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: 4d709843940bc6ccb675fe76f4ca005c Package: cmapR Version: 1.16.0 Depends: R (>= 4.0) Imports: methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle, rmarkdown License: file LICENSE MD5sum: d3b9b99bcb1c52fe3708053ae7d1573b Package: CNAnorm Version: 1.50.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: be306d37791c6a16394dbb4869540048 Package: cn.farms Version: 1.52.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) MD5sum: 82bff55e8074ee442824993a098bd6f8 Package: cn.mops Version: 1.50.0 Depends: R (>= 3.5.0), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: 6e0a26a2bb501eb229b77b68bbe357c4 Package: CNORdt Version: 1.46.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: a224c6f9b98a3e447b7089b68202e8c0 Package: CNORfeeder Version: 1.44.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 5b825d2173849e57f39e9c56001999d8 Package: CNORfuzzy Version: 1.46.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: a9f15dc66c4dd81f73ae7629de72d2ae Package: CNORode Version: 1.46.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: GPL-2 MD5sum: 04b4104384b3a815e3bf57910f7444b2 Package: CNTools Version: 1.60.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: cf5ea7020316071beebbe96a1825b72e Package: CNVfilteR Version: 1.18.0 Depends: R (>= 4.3) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown License: Artistic-2.0 MD5sum: 79c334258e01eff35c3cf4360a6655dc Package: CNVgears Version: 1.12.0 Depends: R (>= 4.1), data.table Imports: ggplot2 Suggests: VariantAnnotation, DelayedArray, knitr, biomaRt, evobiR, rmarkdown, devtools, cowplot, usethis, scales, testthat, GenomicRanges, cn.mops, R.utils License: GPL-3 MD5sum: bb354749ca4ded780d320ab720b376c1 Package: cnvGSA Version: 1.48.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: 56eaa73d3ce8ae4962488b1ad6b88084 Package: CNViz Version: 1.12.0 Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: 187c2b8f7e27c947c65f9c7b66a5e936 Package: CNVMetrics Version: 1.8.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 1e5779cadc22bd63290c0c08961c18d9 Package: CNVPanelizer Version: 1.36.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: 912b570c4b4faa42a19c95f293030ce2 Package: CNVRanger Version: 1.20.0 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod License: Artistic-2.0 MD5sum: df8c4518ba2ddbda8c439d38b0baa6b7 Package: CNVrd2 Version: 1.42.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: 4b258793852edb2d5fc6def80174c0fb Package: CoCiteStats Version: 1.76.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 185ba6ff8f0c0bdcc64cb6ea6b23f73a Package: COCOA Version: 2.18.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: ef76f70fff8f220503b09f46841dbeb4 Package: codelink Version: 1.72.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: 508ca7ceb6376ea023ba75e3303daa40 Package: CODEX Version: 1.36.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: bcc74a3ce9c241e89392e24fe2d4e09e Package: CoGAPS Version: 3.24.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache License: BSD_3_clause + file LICENSE MD5sum: 8b352ff8877393947fb888b49b56d75c Package: cogena Version: 1.38.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 6386f769d7899482ae3d73824038cc32 Package: cogeqc Version: 1.8.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: ee804faec4cd14223ceb9888d74a6ca2 Package: Cogito Version: 1.10.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, GenomeInfoDb, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: f6aa71cf839b22c76f814bf9101e8429 Package: coGPS Version: 1.48.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 6e0aebbf181b749fc2f85433089335c4 Package: cola Version: 2.10.0 Depends: R (>= 4.0.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats, GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 32c0018616c23d24feecc6ffea717a6f Package: comapr Version: 1.8.0 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE MD5sum: 7a28980285a72b9b138628cdc21d402b Package: combi Version: 1.16.0 Depends: R (>= 4.0), DBI Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>= 1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: f466be5f7a891c720b6f1f7723718c18 Package: coMET Version: 1.36.0 Depends: R (>= 4.1.0), grid, utils, biomaRt, Gviz, psych Imports: hash,grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics, showtext License: GPL (>= 2) MD5sum: ca55ba63e140fc3d8e5155607fffaf47 Package: coMethDMR Version: 1.8.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 MD5sum: 725582a4383b838ee0fb10d4fac37ba7 Package: compartmap Version: 1.22.0 Depends: R (>= 4.1.0), SummarizedExperiment, RaggedExperiment, BiocSingular, HDF5Array Imports: GenomicRanges, parallel, grid, ggplot2, reshape2, scales, DelayedArray, rtracklayer, DelayedMatrixStats, Matrix, RMTstat Suggests: covr, testthat, knitr, Rcpp, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: 412af1250f7257813f940adb4a261a64 Package: COMPASS Version: 1.42.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: ccd50246ff995af2048ae6f706b3f50f Package: compcodeR Version: 1.40.0 Depends: R (>= 4.0), sm Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: f993e7b246e2b7509113cf56d006d56a Package: compEpiTools Version: 1.38.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: 904f2fc60c6e78a6110dff1265531919 Package: ComplexHeatmap Version: 2.20.0 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: 9973856410ccbb2675e03537a1e77b8f Package: CompoundDb Version: 1.8.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.9.12), MsCoreUtils, MetaboCoreUtils, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: fc3b46f0113b1fe5cfa53d933cc80edf Package: ComPrAn Version: 1.12.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 7db6144adbfa6a373b05cb0a511c2b4f Package: compSPOT Version: 1.2.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: ec7725d814946255e7c934345df59bf8 Package: concordexR Version: 1.4.0 Depends: R (>= 4.2) Imports: BiocParallel, cli, DelayedArray, ggplot2, Matrix, methods, pheatmap, rlang, scales Suggests: BiocNeighbors, BiocStyle, bluster, covr, knitr, patchwork, rmarkdown, scater, TENxPBMCData, testthat (>= 3.0.0), vdiffr License: Artistic-2.0 MD5sum: cfc302d7985b4b5004db45c8fdcbb2ca Package: condiments Version: 1.12.0 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN License: MIT + file LICENSE MD5sum: 452468352c2d8a357225e4c8d499a56d Package: CONFESS Version: 1.32.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 MD5sum: 4f6e7a1b571409eda89af7db77c35bad Package: consensus Version: 1.22.0 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE MD5sum: ac6d5d8f738ce097bdcbbe7bd62d6e51 Package: ConsensusClusterPlus Version: 1.68.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: f84b2bf9b8aedcc585a19d7466f095df Package: consensusDE Version: 1.22.0 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 31975eedcd210fc7c46b36ca51eaea49 Package: consensusOV Version: 1.26.0 Depends: R (>= 3.6) Imports: Biobase, GSVA (>= 1.50.0), gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods, BiocParallel Suggests: BiocStyle, ggplot2, knitr, rmarkdown, magick License: Artistic-2.0 MD5sum: dd0dc75a6526554469b575900ef11987 Package: consensusSeekeR Version: 1.32.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 708afd198a19306168e4973d812337b4 Package: consICA Version: 2.2.0 Depends: R (>= 4.2.0) Imports: fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat License: MIT + file LICENSE MD5sum: 94b0467a1c163248306cb4ecfc05468c Package: CONSTANd Version: 1.12.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE MD5sum: 1650db23496cfe5620ed69f3fce38e79 Package: conumee Version: 1.38.0 Depends: R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, GenomeInfoDb Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl License: GPL (>= 2) MD5sum: bfa6a9cd77c51d83d8b678f46ec97856 Package: convert Version: 1.80.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: d9e7143d4fa46931373643787e123805 Package: copa Version: 1.72.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 MD5sum: fbc85ad1423f79872cc019c9f3ea6a4b Package: CopyNumberPlots Version: 1.20.0 Depends: R (>= 3.6), karyoploteR Imports: regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat License: Artistic-2.0 MD5sum: fe536e7a2a04a213225d5a97bedcb7c4 Package: coRdon Version: 1.22.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: e937ad745fe2d7826ccdaa360f3ea6e7 Package: CoRegNet Version: 1.42.0 Depends: R (>= 2.14), igraph, shiny, arules, methods Suggests: RColorBrewer, gplots, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 3b6ceba28ec61fc7e569f539e436d9e3 Package: CoreGx Version: 2.8.0 Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) MD5sum: a98fda03da56e7dac20bb27fdf540fa6 Package: Cormotif Version: 1.50.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: 34cf79ddb8c440a6344a0ed490d60633 Package: corral Version: 1.14.0 Imports: ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat License: GPL-2 MD5sum: 607bbac3db28f77e208743fd159448f8 Package: coseq Version: 1.28.0 Depends: R (>= 4.0.0), SummarizedExperiment, S4Vectors Imports: edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2, scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics, stats, methods, compositions, mvtnorm Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: c011ec1c9e24a8825fe35befb4fe43a2 Package: cosmosR Version: 1.12.0 Depends: R (>= 4.1) Imports: CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR Suggests: testthat, knitr, rmarkdown, piano, ggplot2 License: GPL-3 MD5sum: 3fc29b16a7e4c750443a3f991091caa3 Package: COSNet Version: 1.38.0 Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: b998f13b0656478fe5795407faf7f347 Package: COTAN Version: 2.4.4 Depends: R (>= 4.2) Imports: stats, plyr, dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, ggthemes, graphics, parallel, parallelly, tibble, tidyr, BiocSingular, PCAtools, parallelDist, ComplexHeatmap, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, umap, dendextend, zeallot, assertthat, withr Suggests: testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch License: GPL-3 MD5sum: 863b73b1c031302e2b61cc9241e8e200 Package: countsimQC Version: 1.22.0 Depends: R (>= 3.5) Imports: rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods, ragg Suggests: knitr, testthat License: GPL (>= 2) MD5sum: ac0e4384c18563b45dc67c51eb891af2 Package: covEB Version: 1.30.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: 299c8076a82ebf84bb9fc2472bc00ad7 Package: CoverageView Version: 1.42.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools License: Artistic-2.0 MD5sum: 01b56fab3cd870967113edc39db7ac81 Package: covRNA Version: 1.30.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: b7d5ffd977f0a9c7f41933dc992a730b Package: cpvSNP Version: 1.36.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 1eebbfc5294b8a0abbba8ec959261e4a Package: cqn Version: 1.50.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 MD5sum: 927189e67a1984ac8f503b4712b881ad Package: CRImage Version: 1.52.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: 3963b10db6f8869099446d35122ba088 Package: CRISPRball Version: 1.0.0 Depends: R (>= 4.4.0), shinyBS Imports: DT, shiny, grid, ComplexHeatmap, InteractiveComplexHeatmap, graphics, stats, ggplot2, plotly, shinyWidgets, shinycssloaders, shinyjqui, dittoSeq, matrixStats, colourpicker, shinyjs, MAGeCKFlute, circlize, PCAtools, utils, grDevices, htmlwidgets, methods Suggests: BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 92430d258bffb86faa6afb47b8cee96a Package: crisprBase Version: 1.8.0 Depends: utils, methods, R (>= 4.1) Imports: BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 448886de3a326e9258674eeda09336fa Package: crisprBowtie Version: 1.8.0 Depends: methods Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: c405a4f591831d5b93d19e1bcafe37bf Package: crisprBwa Version: 1.8.0 Depends: methods Imports: BiocGenerics, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, Rbwa, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE OS_type: unix MD5sum: b7b0a3ad940ad38d2accc032761fd4bb Package: crisprDesign Version: 1.6.0 Depends: R (>= 4.2.0), crisprBase (>= 1.1.3) Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6), GenomeInfoDb, GenomicFeatures, GenomicRanges (>= 1.38.0), IRanges, Matrix, MatrixGenerics, methods, rtracklayer, S4Vectors, stats, txdbmaker, utils, VariantAnnotation Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE MD5sum: f21138623e4966d9b8f040492a207040 Package: crisprScore Version: 1.8.0 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: basilisk (>= 1.9.2), basilisk.utils (>= 1.9.1), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 8f543fb91f670b7423d1fdf953e18ba0 Package: CRISPRseek Version: 1.44.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat License: GPL (>= 2) MD5sum: aaed17d23a6364c2d676204924082340 Package: crisprseekplus Version: 1.30.0 Depends: R (>= 3.3.0), shiny, shinyjs, CRISPRseek Imports: DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures, BiocManager, BSgenome, AnnotationDbi, hash Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: eb138a140ba3656bf68d6cfe01dc7f0a Package: crisprShiny Version: 1.0.0 Depends: R (>= 4.4.0), shiny Imports: BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign, crisprScore, crisprViz, DT, GenomeInfoDb, htmlwidgets, methods, pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 License: MIT + file LICENSE MD5sum: 6d8e8bfe1bdae6b5570f9a324bdd3e8c Package: CrispRVariants Version: 1.32.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: ab6cba88e558777469880fb7699d16cb Package: crisprVerse Version: 1.6.0 Depends: R (>= 4.2.0) Imports: BiocManager, cli, crisprBase, crisprBowtie, crisprScore, crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils Suggests: BiocStyle, knitr, testthat License: MIT + file LICENSE MD5sum: f8fcd40dc93629da21241b56b63f7773 Package: crisprViz Version: 1.6.0 Depends: R (>= 4.2.0), crisprBase (>= 0.99.15), crisprDesign (>= 0.99.77) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors, txdbmaker Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE MD5sum: d2ec9120d76c33a666c6aa82b0ea6c39 Package: crlmm Version: 1.62.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit License: Artistic-2.0 MD5sum: 0ce42f3bae9c76e22ad21bdf4beb5d15 Package: crossmeta Version: 1.30.0 Depends: R (>= 4.0) Imports: affy (>= 1.52.0), affxparser (>= 1.46.0), AnnotationDbi (>= 1.36.2), Biobase (>= 2.34.0), BiocGenerics (>= 0.20.0), BiocManager (>= 1.30.4), DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), edgeR, fdrtool (>= 1.2.15), GEOquery (>= 2.40.0), limma (>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), miniUI (>= 0.1.1), methods, oligo (>= 1.38.0), reader(>= 1.0.6), RCurl (>= 1.95.4.11), RSQLite (>= 2.1.1), stringr (>= 1.2.0), sva (>= 3.22.0), shiny (>= 1.0.0), shinyjs (>= 2.0.0), shinyBS (>= 0.61), shinyWidgets (>= 0.5.3), shinypanel (>= 0.1.0), tibble, XML (>= 3.98.1.17), readxl (>= 1.3.1) Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat License: MIT + file LICENSE MD5sum: 061e8fcecf81f4738e3a1b5f3b48ee0f Package: CSAR Version: 1.56.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 7319fab6c0ac0c2600ab0225b3d3ee4b Package: csaw Version: 1.38.0 Depends: R (>= 3.5.0), GenomicRanges, SummarizedExperiment Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: c2b7d1f9d74ef2280ca3e6a0a70f5dc7 Package: csdR Version: 1.10.0 Depends: R (>= 4.1.0) Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp LinkingTo: Rcpp Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr License: GPL-3 MD5sum: 9716fe689f1730c4159bea95ed36c68a Package: CSSQ Version: 1.16.0 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, markdown License: Artistic-2.0 MD5sum: 01e2456014ba71c6379b25e94cfdc87c Package: ctc Version: 1.78.0 Depends: amap License: GPL-2 MD5sum: 52c060bc658fd39d19509b17be3201df Package: CTdata Version: 1.4.0 Depends: R (>= 4.2) Imports: ExperimentHub, utils Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: bd16df3b68be33a527bd28c0cc1982a7 Package: CTDquerier Version: 2.12.0 Depends: R (>= 4.1) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0b772a2ed6a7efeda2965b1042e72763 Package: CTexploreR Version: 1.0.0 Depends: R (>= 4.3), CTdata Imports: BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 452f376b48d0d0b14362ef495b3ab2d3 Package: cTRAP Version: 1.22.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE MD5sum: 8ca0fe874c1e03170068491d389d8a98 Package: ctsGE Version: 1.30.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: 89f6ae28ee059c1d2b407333c5d91e41 Package: CTSV Version: 1.6.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 MD5sum: d034e7f6849e30e2b6e35544564d7116 Package: cummeRbund Version: 2.46.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 MD5sum: 6411a883f48a083be3e9259c172e16ec Package: CuratedAtlasQueryR Version: 1.2.0 Depends: R (>= 4.2.0) Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot License: GPL-3 MD5sum: 66810b72f8b08f70a15c6d0be2e9e1b1 Package: customCMPdb Version: 1.14.0 Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: f8489e7dfcf2bbf82d0dc47cd999f80f Package: customProDB Version: 1.44.0 Depends: R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt (>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, txdbmaker, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: e6bbf999d6ff1fa1f224fa75992daa39 Package: cyanoFilter Version: 1.12.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE MD5sum: efbfa2017e183f80bb21c807808db13b Package: cycle Version: 1.58.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: 16559ecaf6e3c53af66ac90358b91e53 Package: cydar Version: 1.28.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: 4b27607675ae97d90e884e44eb2019cd Package: cypress Version: 1.0.0 Depends: R(>= 4.4.0) Imports: stats, abind, sirt, MASS,TOAST, tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071 Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase License: GPL-2 | GPL-3 MD5sum: 7c9de6fccf9619609a7518c3ce53d83f Package: CytoDx Version: 1.24.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: a35b4baff2e0fa68029abb0e6b5e900e Package: CyTOFpower Version: 1.10.0 Depends: R (>= 4.1) Imports: CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods, rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix, SummarizedExperiment, tibble, tidyr Suggests: testthat (>= 3.0.0), BiocStyle, knitr License: LGPL-3 MD5sum: 36f583605eb809bcc8bb2ba26844022e Package: cytofQC Version: 1.4.0 Imports: CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes, matrixStats, randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot License: Artistic-2.0 MD5sum: 363c39307cbf5312961c65b0e928589c Package: CytoGLMM Version: 1.12.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: 9879171b2f33a027ad72420bef7b7115 Package: cytoKernel Version: 1.10.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap, circlize, ashr, data.table, BiocParallel, dplyr, stats, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 7aa698d5873bf25a573b0beb970fadd7 Package: cytolib Version: 2.16.0 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.84.0.0), RProtoBufLib(>= 2.13.1),Rhdf5lib Suggests: knitr, rmarkdown License_restricts_use: no MD5sum: 618a1e88b451213de5c1e975a50f7be4 Package: cytomapper Version: 1.16.0 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: bbd5e16d6c2b71a423d106ec93f967bd Package: CytoMDS Version: 1.0.0 Depends: R (>= 4.3) Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: 95779bdbf412c459f476bde8f7f6d641 Package: cytoMEM Version: 1.8.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 3536dfd1bfb010d4909397072fd188d2 Package: CytoML Version: 2.16.0 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats, tibble LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel License_restricts_use: no MD5sum: 0c16f111a1c483dfc0f303878fa0933d Package: CytoPipeline Version: 1.4.0 Depends: R (>= 4.3) Imports: methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1), ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI, diagram, jsonlite, scales Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, reshape2, dplyr License: GPL-3 MD5sum: 9de1d3b57e46be1c48a1b7da897ba0c1 Package: CytoPipelineGUI Version: 1.2.0 Depends: R (>= 4.3), CytoPipeline Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: 80ffdce93eeaa706d0e74d98911b4ceb Package: cytoviewer Version: 1.4.0 Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: e8de5280432a0f9d67504e91128accc3 Package: dada2 Version: 1.32.0 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 MD5sum: 6c35fee2689faae568e0a85d67f4c90e Package: dagLogo Version: 1.42.0 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack, httr Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: d1e716d3b0b31dbeb925b0a201991f0e Package: daMA Version: 1.76.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: eba720610bb5f8212b99540e2cafe773 Package: DAMEfinder Version: 1.16.0 Depends: R (>= 4.0) Imports: stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: f8d7d2afc40484af4fe3ab8cf33ba660 Package: DaMiRseq Version: 2.16.0 Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: ab9df636eb47ace265f0d02df907749a Package: Damsel Version: 1.0.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, Biostrings, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene License: MIT + file LICENSE MD5sum: 537517d7c53561d3126f3dd8d0018eef Package: DAPAR Version: 1.36.2 Depends: R (>= 4.3.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 62aeb5fb7241a6497e999e1bc2e4427d Package: dar Version: 1.0.0 Depends: R (>= 4.4.0) Imports: cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR, waldo Suggests: ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 40aa2a457bf9f9fc9564f36a3e82d275 Package: DART Version: 1.52.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 6a2eb3d866b78729b16efcd698db9b33 Package: dcanr Version: 1.20.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 44bfcccd135da25066b700a12cc8482f Package: DCATS Version: 1.2.0 Depends: R (>= 4.1.0), stats Imports: MCMCpack, matrixStats, robustbase, aod, e1071 Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 13fdd90bfbcb09580fa3ab1b81ccd42b Package: dce Version: 1.12.0 Depends: R (>= 4.1) Imports: stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, magrittr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger, shadowtext Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL License: GPL-3 MD5sum: 7770780124652d054e926f214ae32378 Package: dcGSA Version: 1.32.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 61ff49e86155c820e397bc4ae5ca2854 Package: ddCt Version: 1.60.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 MD5sum: 1b8a425836d935eebb258aab91526a09 Package: ddPCRclust Version: 1.24.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 MD5sum: 41b8a040fe1f1280109b4709b0206cbc Package: dearseq Version: 1.16.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, scattermore, stats, statmod, survey, tibble, viridisLite Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: e23522f024e87aeb0253512e87d29986 Package: debCAM Version: 1.22.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: 803e14d2023bc04665d7a6636c7ab523 Package: debrowser Version: 1.32.0 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, knitr License: GPL-3 + file LICENSE MD5sum: 6326af48ca0789739412ce88120daa0a Package: DECIPHER Version: 3.0.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 MD5sum: 259850d23f09e3bd5dbe1941a02a03a5 Package: DeconRNASeq Version: 1.46.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: 4ee67853352cc9d2803840dfb7731f8b Package: decontam Version: 1.24.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: 7b5b5c5740b5f15080d321189a8f3dff Package: decontX Version: 1.2.0 Depends: R (>= 4.3.0) Imports: celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3), MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.2.0), S4Vectors, scater, Seurat, SingleCellExperiment, SummarizedExperiment, withr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a2d104eee0df5c11a8304623d1d4f384 Package: deconvR Version: 1.10.0 Depends: R (>= 4.1), data.table (>= 1.14.0) Imports: S4Vectors (>= 0.30.0), methylKit (>= 1.18.0), IRanges (>= 2.26.0), GenomicRanges (>= 1.44.0), BiocGenerics (>= 0.38.0), stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR License: Artistic-2.0 MD5sum: 20dc1b2ed65f7abe9af4f70aab009a67 Package: DeepPINCS Version: 1.12.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 799ea1637d440795949a3047ba384e27 Package: deepSNV Version: 1.50.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.27.6), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 57fb9b5b06658e5b7b3e49555fc5647b Package: DEFormats Version: 1.32.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: b46b0cf757646e12cf9f0a6ff37214fb Package: DegCre Version: 1.0.0 Depends: R (>= 4.4) Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, GenomeInfoDb, IRanges, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, org.Hs.eg.db, BiocStyle, magick, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 77ccaca14a9e85d1f0d29d42d4f8552e Package: DegNorm Version: 1.14.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: e66de0bfddb9a6acf0ee67fc9859400d Package: DEGreport Version: 1.40.1 Depends: R (>= 4.0.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, stringi, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: befb1abba175dcd49b5e09dacea04d54 Package: DEGseq Version: 1.58.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 9aee37eb49a3ade992fe90695907897a Package: DelayedArray Version: 0.30.1 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.43.4), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3), S4Arrays (>= 1.3.5), SparseArray (>= 1.1.10) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: f7bbf35178a6fd513ded1a33bff4d4c7 Package: DelayedDataFrame Version: 1.20.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray License: GPL-3 MD5sum: c5d79bd6373af3e759204878edd8f545 Package: DelayedMatrixStats Version: 1.26.0 Depends: MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.27.10) Imports: methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10) Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) License: MIT + file LICENSE MD5sum: a916486f32889618a733f6187a073b96 Package: DelayedRandomArray Version: 1.12.0 Depends: DelayedArray (>= 0.27.2) Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 MD5sum: 068fedfbba7f5c51d252b3c22d192425 Package: DelayedTensor Version: 1.10.0 Depends: R (>= 4.1.0) Imports: methods, utils, DelayedArray, HDF5Array, BiocSingular, rTensor, DelayedRandomArray, irlba, Matrix, einsum, Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate License: Artistic-2.0 MD5sum: eac60c59ee4bef363defd3e8ce5fac1f Package: DELocal Version: 1.4.0 Imports: DESeq2, dplyr, reshape2, limma, SummarizedExperiment, ggplot2, matrixStats, stats Suggests: biomaRt, knitr, rmarkdown, stringr, BiocStyle License: MIT + file LICENSE MD5sum: afe257d37863fdc1fe3b1ef728ab91d1 Package: deltaCaptureC Version: 1.18.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: d1b1557073c4cef0f5ea734f67a06f96 Package: deltaGseg Version: 1.44.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: e100ca911905182c11abba55f41b67c2 Package: DeMAND Version: 1.34.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: 808a31276976fb9ce011ea7be5c8f4d3 Package: DeMixT Version: 1.20.0 Depends: R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend, psych, sva Imports: matrixStats, stats, truncdist, base64enc, ggplot2 LinkingTo: Rcpp License: GPL-3 MD5sum: 2eb82ed8297d32e81bfd1ee75b57c0e6 Package: demuxmix Version: 1.6.0 Depends: R (>= 4.0.0) Imports: stats, MASS, Matrix, ggplot2, gridExtra, methods Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5a42bc15a3f84449044e4095ec050a17 Package: demuxSNP Version: 1.2.0 Depends: R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb Imports: MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr Suggests: knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat License: GPL-3 MD5sum: abb98803987ddadc663e77f27ad8a561 Package: densvis Version: 1.14.0 Imports: Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat License: MIT + file LICENSE MD5sum: e649ed8ece7e9b7c736dff790e77b065 Package: DEP Version: 1.26.0 Depends: R (>= 3.5) Imports: ggplot2, dplyr, purrr, readr, tibble, tidyr, SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool, ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid, stats, imputeLCMD, cluster Suggests: testthat, enrichR, knitr, BiocStyle License: Artistic-2.0 MD5sum: c11615d0f65003b2cd609b0179175def Package: DepecheR Version: 1.20.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics (>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), FNN (>= 1.1.3), robustbase (>= 0.93.5), gmodels (>= 2.18.1), collapse (>= 1.9.2), ClusterR (>= 1.3.2) LinkingTo: Rcpp, RcppEigen Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 7176d903ddf6f90086e6a63c41e21828 Package: DepInfeR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: matrixStats, glmnet, stats, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm License: GPL-3 MD5sum: 8d394195574c17dcaa18264bc5d83916 Package: DEqMS Version: 1.22.0 Depends: R(>= 3.5),graphics,stats,ggplot2,matrixStats,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,farms,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: 03622ae2c722338f41f0581fa51fdc38 Package: derfinder Version: 1.38.0 Depends: R (>= 3.5.0) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>= 0.23.19), stats, utils Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: 7059b04ab2fb49d37dad751add82d13a Package: derfinderHelper Version: 1.38.0 Depends: R(>= 3.2.2) Imports: IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2) Suggests: sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), RefManageR, rmarkdown (>= 0.3.3), testthat, covr License: Artistic-2.0 MD5sum: 7aee818019ba176192c2bfcbc206c457 Package: derfinderPlot Version: 1.38.0 Depends: R(>= 3.2) Imports: derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>= 1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28), limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>= 0.9.38), scales, utils Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: 509c11bd8b4bcc67a666676c1be8a3ef Package: DEScan2 Version: 1.24.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19), SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 MD5sum: 7716c2f681ecca9bdc8b5a29f73245a3 Package: DESeq2 Version: 1.44.0 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats, methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0), MatrixGenerics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager License: LGPL (>= 3) MD5sum: 212ebd1328a798cf6550ec9b97864929 Package: DEsingle Version: 1.24.0 Depends: R (>= 3.4.0) Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0), Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: 37419f1882f078e16a431c6b7410f92b Package: DESpace Version: 1.4.0 Depends: R (>= 4.3.0) Imports: edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2, ggpubr, scales, SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat, cowplot, ggforce, ggnewscale, patchwork, BiocParallel, methods Suggests: knitr, rmarkdown, testthat, BiocStyle, ExperimentHub, concaveman, spatialLIBD, purrr, scuttle, utils License: GPL-3 MD5sum: c35844e14d654b88d2944066be8ac58a Package: destiny Version: 3.18.0 Depends: R (>= 3.4.0) Imports: methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods, Biobase, BiocGenerics, SummarizedExperiment, SingleCellExperiment, ggplot2, ggplot.multistats, rlang, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d LinkingTo: Rcpp, RcppEigen, grDevices Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr Enhances: rgl, SingleCellExperiment License: GPL-3 MD5sum: bcb23d8268a5855633e8a8ee5b15ee73 Package: DEsubs Version: 1.30.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: 3d6d1004f945c6c2341c7ca8d0e5a44c Package: DEWSeq Version: 1.18.0 Depends: R(>= 4.0.0), R.utils, DESeq2, BiocParallel Imports: BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb, GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats, utils Suggests: knitr, tidyverse, rmarkdown, testthat, BiocStyle, IHW License: LGPL (>= 3) MD5sum: 0682729709befd2b4db333fcb1f1f005 Package: DExMA Version: 1.12.0 Depends: R (>= 4.1), DExMAdata Imports: Biobase, GEOquery, impute, limma, pheatmap, plyr, scales, snpStats, sva, swamp, stats, methods, utils, bnstruct, RColorBrewer, grDevices Suggests: BiocStyle, qpdf, BiocGenerics, RUnit License: GPL-2 MD5sum: 718efb48e96ddbcf381b9f9db70f78e0 Package: DEXSeq Version: 1.50.0 Depends: BiocParallel, Biobase, SummarizedExperiment, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.39.6), AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18) Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter Suggests: GenomicFeatures, txdbmaker, pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi License: GPL (>= 3) MD5sum: cabae24decb5cd2229f7c755f4958107 Package: DFP Version: 1.62.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 MD5sum: a8d919138ee4905559aa417e9b4f4b77 Package: DiffBind Version: 3.14.0 Depends: R (>= 4.0), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools (>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP LinkingTo: Rhtslib (>= 1.99.1), Rcpp Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid License: Artistic-2.0 MD5sum: b64db98c1eb2607b36b43b235f54bb83 Package: diffcoexp Version: 1.24.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery, RUnit License: GPL (> 2) MD5sum: 9a9fc10d2fec854c9a52fd9f1d9b39d8 Package: diffcyt Version: 1.24.0 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: 1a18b23c619603019e7ddd8246873d23 Package: DifferentialRegulation Version: 2.2.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2, tximport, gridExtra LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 0f37f703c38b565cd3758cbdd0b4ceae Package: diffGeneAnalysis Version: 1.86.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: a0a4bc1b631b856f42d926d72bd7c81f Package: diffHic Version: 1.36.1 Depends: R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer LinkingTo: Rhtslib (>= 1.13.1), zlibbioc, Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat License: GPL-3 MD5sum: d8a109972fae42d6fa3271484d27024e Package: DiffLogo Version: 2.28.0 Depends: R (>= 3.4), stats, cba Imports: grDevices, graphics, utils, tools Suggests: knitr, testthat, seqLogo, MotifDb License: GPL (>= 2) MD5sum: c87101c30749c042166b7a18cdb712db Package: diffuStats Version: 1.24.0 Depends: R (>= 3.4) Imports: grDevices, stats, methods, Matrix, MASS, checkmate, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils License: GPL-3 MD5sum: 77f7c186b556b05a5fa7d7abbdbe4b82 Package: diffUTR Version: 1.12.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq, GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap, ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr, matrixStats, IRanges, ensembldb, viridisLite Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 01a1265e4f25fe7e58a3d66ee8895c45 Package: diggit Version: 1.36.0 Depends: R (>= 3.0.2), Biobase, methods Imports: ks, viper(>= 1.3.1), parallel Suggests: diggitdata License: file LICENSE MD5sum: 1bad4dc8524214bd1e027d78ed5036cf Package: Dino Version: 1.10.0 Depends: R (>= 4.0.0) Imports: BiocParallel, BiocSingular, SummarizedExperiment, SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats, parallel, scran, grDevices, stats, methods Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin License: GPL-3 MD5sum: 39d90788822e8aa754e2ba23ba26583a Package: dinoR Version: 1.0.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR, GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr, tibble, tidyr, tidyselect Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: dc3f8996557f26b53bbc4928b550fac2 Package: Director Version: 1.30.0 Depends: R (>= 4.0) Imports: htmltools, utils, grDevices License: GPL-3 + file LICENSE MD5sum: 51977e6697ab23993f61462b3054b468 Package: dir.expiry Version: 1.12.0 Imports: utils, filelock Suggests: rmarkdown, knitr, testthat, BiocStyle License: GPL-3 MD5sum: 0cce6d27a9eb408846e0c6f8ddbfb1da Package: DirichletMultinomial Version: 1.46.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, xtable License: LGPL-3 MD5sum: 0c1b834dee717db2e9e39e46a2ac5efe Package: discordant Version: 1.28.0 Depends: R (>= 4.1.0) Imports: Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr, methods, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: abe4c42d70aee4b1e3542de26440b072 Package: DiscoRhythm Version: 1.20.0 Depends: R (>= 3.6.0) Imports: matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table, ggplot2, ggExtra, dplyr, broom, shiny, shinyBS, shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown, knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 MD5sum: 4c185e21728e2bc5ae9a1c9be0a273dd Package: distinct Version: 1.16.0 Depends: R (>= 4.3) Imports: Rcpp, stats, SummarizedExperiment, SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle License: GPL (>= 3) MD5sum: 85dd14452ea2b44c9eded42ebd8c3f53 Package: dittoSeq Version: 1.16.0 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran License: MIT + file LICENSE MD5sum: c55bca66f15eaa39c537e137d8e73e3f Package: divergence Version: 1.20.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 5febea625dfd1eef9f4eced67b1eb1ba Package: dks Version: 1.50.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: 4e23a93d66e68bb0e07abe8486e8f9c9 Package: DMCFB Version: 1.18.0 Depends: R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges Imports: utils, stats, speedglm, MASS, data.table, splines, arm, rtracklayer, benchmarkme, tibble, matrixStats, fastDummies, graphics Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 96dd41dadb858916a732b4e5118b0558 Package: DMCHMM Version: 1.26.0 Depends: R (>= 4.1.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges, fdrtool Imports: utils, stats, grDevices, rtracklayer, multcomp, calibrate, graphics Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 771d310d185eb9e22e87b53fb363f438 Package: DMRcaller Version: 1.36.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10) Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: e60d58a549267cb7da5c3f35dc6d8ce9 Package: DMRcate Version: 3.0.4 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest License: file LICENSE MD5sum: 37c9730cb6a1e201edfe383bca11ccc0 Package: dmrseq Version: 1.24.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 3cc1dedfd3970469c5eec83abc593f7e Package: DNABarcodeCompatibility Version: 1.20.0 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats, utils, methods Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE MD5sum: 18ae55d3f0059e57dd4aeb3e39e3bf42 Package: DNABarcodes Version: 1.34.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: db9133b8d7db339f5af0817021229825 Package: DNAcopy Version: 1.78.0 License: GPL (>= 2) MD5sum: eec39bbe937c6cdffcf48b0b1181f04f Package: DNAfusion Version: 1.6.0 Depends: R (>= 4.2.0) Imports: bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle License: GPL-3 MD5sum: 04d8c07c3d570263ae15aa5ab2a4e351 Package: DNAshapeR Version: 1.32.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 MD5sum: b25f22936bbcc1005eba1c2ec68b619b Package: DominoEffect Version: 1.24.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, pwalign, SummarizedExperiment, VariantAnnotation, AnnotationDbi, GenomeInfoDb, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 02dac724cf8119ddc287925f17a7d97b Package: doppelgangR Version: 1.32.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: a8982db253289a6a16f77ed83ceef9a4 Package: Doscheda Version: 1.26.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: b9dd27213a27bc8ac0877ff67066e634 Package: DOSE Version: 3.30.1 Depends: R (>= 3.5.0) Imports: AnnotationDbi, HDO.db, BiocParallel, fgsea, ggplot2, GOSemSim (>= 2.27.1), methods, qvalue, reshape2, stats, utils, yulab.utils Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, HPO.db, MPO.db, testthat License: Artistic-2.0 MD5sum: 8635e6da6be86438b931edd5ad2b8ed8 Package: doseR Version: 1.20.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: e5c6f8872ccb8b382bc1b6da2aea2f46 Package: doubletrouble Version: 1.4.0 Depends: R (>= 4.2.0) Imports: syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures, BiocParallel Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: a0a25a321695cba440c4e37e9f4f14eb Package: dpeak Version: 1.16.0 Depends: R (>= 4.0.0), methods, stats, utils, graphics, Rcpp Imports: MASS, IRanges, BSgenome, grDevices, parallel LinkingTo: Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805 License: GPL (>= 2) MD5sum: 830c4c199cb287d85b472b7d67cc7742 Package: drawProteins Version: 1.24.0 Depends: R (>= 4.0) Imports: ggplot2, httr, dplyr, readr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: bbf6d2f8a9e0239950cf577f683395b2 Package: dreamlet Version: 1.2.1 Depends: R (>= 4.3.0), variancePartition (>= 1.33.11), SingleCellExperiment, ggplot2 Imports: edgeR, SummarizedExperiment, DelayedMatrixStats, sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr, GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52), ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, rlang, BiocGenerics, DelayedArray, gtools, reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS, Rdpack, utils, stats LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, scater, scuttle License: Artistic-2.0 MD5sum: 79fa053711e6741ef1e30be636e300f3 Package: DRIMSeq Version: 1.32.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 0667606fccc3bc288971ae209505c5e2 Package: DriverNet Version: 1.44.0 Depends: R (>= 2.10), methods License: GPL-3 MD5sum: f1bf8473fab0635759df79963da11848 Package: DropletUtils Version: 1.24.0 Depends: SingleCellExperiment Imports: utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, DelayedArray, DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle LinkingTo: Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles License: GPL-3 MD5sum: 5852acd6f5e30e39f4a10dcba53a5266 Package: drugTargetInteractions Version: 1.12.0 Depends: methods, R (>= 4.1) Imports: utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 License: Artistic-2.0 MD5sum: 90992d5e5c1d51ffd1e3a9ded2168581 Package: DSS Version: 2.52.0 Depends: R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel Imports: utils, graphics, stats, splines Suggests: BiocStyle, knitr, rmarkdown, edgeR License: GPL MD5sum: 5acdeab8babea59efe1374dd89c875f1 Package: dStruct Version: 1.10.0 Depends: R (>= 4.1) Imports: zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors, rlang, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 3faae92f169a31ca39fe04206747b2c0 Package: DTA Version: 2.50.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 MD5sum: f3acc2bf518cd79c195ce6cb003f95d5 Package: dupRadar Version: 1.34.0 Depends: R (>= 3.2.0) Imports: Rsubread (>= 1.14.1), KernSmooth Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub License: GPL-3 MD5sum: 504611084af865361223414ca7f5e107 Package: dyebias Version: 1.64.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 MD5sum: 6f0fbdcc04aef6923aeb80b0c91081d9 Package: DynDoc Version: 1.82.0 Depends: methods, utils Imports: methods License: Artistic-2.0 MD5sum: 1280f00741fc32a266d9df57c31c1929 Package: easier Version: 1.10.0 Depends: R (>= 4.2.0) Imports: progeny, easierData, dorothea (>= 1.6.0), decoupleR, quantiseqr, ROCR, grDevices, stats, graphics, ggplot2, ggpubr, DESeq2, utils, dplyr, tidyr, tibble, matrixStats, rlang, BiocParallel, reshape2, rstatix, ggrepel, magrittr, coin Suggests: knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper License: MIT + file LICENSE MD5sum: bddf3a55d844abdf2c1918efed159a3c Package: EasyCellType Version: 1.6.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang, stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, vctrs (>= 0.6.4), BiocStyle Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools, BiocStyle License: Artistic-2.0 MD5sum: ae5498421abae1f568f6b6dc8b8527f0 Package: easylift Version: 1.2.0 Depends: GenomicRanges, BiocFileCache Imports: rtracklayer, GenomeInfoDb, R.utils, tools, methods Suggests: testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 86c227f1438d1fd82c04afb7ef4f2ef8 Package: easyreporting Version: 1.16.0 Depends: R (>= 3.5.0) Imports: rmarkdown, methods, tools, shiny, rlang Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod License: Artistic-2.0 MD5sum: 2f1c67523e0d20a276998c4621add715 Package: easyRNASeq Version: 2.39.0 Imports: Biobase (>= 2.50.0), BiocFileCache (>= 1.14.0), BiocGenerics (>= 0.36.0), BiocParallel (>= 1.24.1), biomaRt (>= 2.46.0), Biostrings (>= 2.58.0), edgeR (>= 3.32.0), GenomeInfoDb (>= 1.26.0), genomeIntervals (>= 1.46.0), GenomicAlignments (>= 1.26.0), GenomicRanges (>= 1.42.0), SummarizedExperiment (>= 1.20.0), graphics, IRanges (>= 2.24.0), LSD (>= 4.1-0), locfit, methods, parallel, rappdirs (>= 0.3.1), Rsamtools (>= 2.6.0), S4Vectors (>= 0.28.0), ShortRead (>= 1.48.0), utils Suggests: BiocStyle (>= 2.18.0), BSgenome (>= 1.58.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) License: Artistic-2.0 MD5sum: e1cf46ba710f00ad455a29e43c7ea12b Package: EBarrays Version: 2.68.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) MD5sum: a823c1476fc3eec9e9ec1c441adde2df Package: EBcoexpress Version: 1.48.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) MD5sum: 4af6247f38ef10fc5bbc2a2c188756af Package: EBImage Version: 4.46.0 Depends: methods Imports: BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils, htmltools, htmlwidgets, RCurl Suggests: BiocStyle, digest, knitr, rmarkdown, shiny License: LGPL MD5sum: 117ae7fb00393bcfcd9f2f7094dd542b Package: EBSEA Version: 1.32.0 Depends: R (>= 4.0.0) Imports: DESeq2, graphics, stats, EmpiricalBrownsMethod Suggests: knitr, rmarkdown License: GPL-2 MD5sum: d83ef392a9c0420a0c00fc31f78c9635 Package: EBSeq Version: 2.2.0 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0) LinkingTo: Rcpp,RcppEigen,BH License: Artistic-2.0 MD5sum: 6d41617f2030b783ef97f0bdb3ba9d7f Package: ecolitk Version: 1.76.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) MD5sum: 42dc3d49f2c50396eb762f27c042618b Package: EDASeq Version: 2.38.0 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown License: Artistic-2.0 MD5sum: e1b11c99a20ea1a2d20e9b8cb021e357 Package: edge Version: 2.36.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE MD5sum: 90e6d138ff6086f409efca8feca26f26 Package: edgeR Version: 4.2.0 Depends: R (>= 3.6.0), limma (>= 3.41.5) Imports: methods, graphics, stats, utils, locfit, Rcpp LinkingTo: Rcpp Suggests: jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject License: GPL (>= 2) MD5sum: acce40c1586736077fe66c59e8977e74 Package: EDIRquery Version: 1.4.0 Depends: R (>= 4.2.0) Imports: tibble (>= 3.1.6), tictoc (>= 1.0.1), utils (>= 4.1.3), stats (>= 4.1.3), readr (>= 2.1.2), InteractionSet (>= 1.22.0), GenomicRanges (>= 1.46.1) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 02d5fb73a34a9bc2afe85811c80a8279 Package: eds Version: 1.6.0 Depends: Matrix Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, tximportData, testthat (>= 3.0.0) License: GPL-2 MD5sum: 9c09e5639e3f98f8cc6d0dfb05a6ddb6 Package: eegc Version: 1.30.0 Depends: R (>= 3.4.0) Imports: R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR, DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db, org.Mm.eg.db, limma, DOSE, AnnotationDbi Suggests: knitr License: GPL-2 MD5sum: a1e846ca0803dec69d0b62972b45f39e Package: EGAD Version: 1.32.0 Depends: R(>= 3.5) Imports: gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo, igraph, plyr, MASS, RCurl, methods Suggests: knitr, testthat, rmarkdown, markdown License: GPL-2 MD5sum: d3bdeb702e5170ab591dfbe475e77941 Package: EGSEA Version: 1.32.0 Depends: R (>= 4.3.0), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO (>= 2.16.0), pathview (>= 1.4.2) Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0), limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1), htmlwidgets, plotly, DT Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: e68acbe9010341048afee95113d56780 Package: eiR Version: 1.44.0 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite License: Artistic-2.0 MD5sum: f5eb2d18285953c56f614c82d9981f94 Package: eisaR Version: 1.16.0 Depends: R (>= 4.1) Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer License: GPL-3 MD5sum: bda228981558622cb81f1e6d8ce6aaca Package: ELMER Version: 2.28.0 Depends: R (>= 3.4.0), ELMER.data (>= 2.9.3) Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer (>= 1.61.2), DelayedArray Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData License: GPL-3 MD5sum: 851fe8082ce9bdd93b2993411624266a Package: EMDomics Version: 2.34.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: 4e12eb22c05aba54495b85a8bb8d3e32 Package: EmpiricalBrownsMethod Version: 1.32.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: cceff0aceb9e8b19ae289329c8576161 Package: EnhancedVolcano Version: 1.22.0 Depends: ggplot2, ggrepel Imports: methods Suggests: ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown License: GPL-3 MD5sum: c7caacb4686877ee2df40569b09bf540 Package: EnMCB Version: 1.16.0 Depends: R (>= 4.0) Imports: survivalROC, glmnet, rms, mboost, Matrix, igraph, methods, survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown License: GPL-2 MD5sum: 6b064124c490c58c823c699541e18ece Package: ENmix Version: 1.40.2 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats,R (>= 3.5.0) Imports: grDevices,graphics,matrixStats,methods,utils,irlba, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges,gtools, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: f76bbc2cba7c16dd1939b6b8dc6cfa08 Package: EnrichedHeatmap Version: 1.34.0 Depends: R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: 64f6145ae46ae3be8b289e779d71412a Package: EnrichmentBrowser Version: 2.34.1 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod License: Artistic-2.0 MD5sum: 2fd340f1975cfd900c61502d8b1ff2ea Package: enrichplot Version: 1.24.0 Depends: R (>= 3.5.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.16.0), ggfun (>= 0.1.3), ggnewscale, ggplot2, ggraph, graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, shadowtext, GOSemSim, magrittr, ggtree, yulab.utils (>= 0.0.8) Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: ef84661d7c94bd93194bc1785d8679b6 Package: enrichViewNet Version: 1.2.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, testthat License: Artistic-2.0 MD5sum: a97da845c8ea67c26b8616c63a0e5926 Package: ensembldb Version: 2.28.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18), GenomicFeatures (>= 1.49.6), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: 731c00c97d507bfaadce5e91af36956b Package: epialleleR Version: 1.12.0 Depends: R (>= 4.1) Imports: stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, data.table, Rcpp LinkingTo: Rcpp, BH, Rhtslib, zlibbioc Suggests: RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra License: Artistic-2.0 MD5sum: 0d17c54a15374c9ba754e5716aebbdf1 Package: epidecodeR Version: 1.12.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: a2526034cb083a43d7b1e4fd56b39c9e Package: EpiDISH Version: 2.20.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: f41f3966df529c01ecc0c62d229e3569 Package: epigenomix Version: 1.44.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: f5ce31661e1283021fd6226745b28fc0 Package: epigraHMM Version: 1.12.0 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE MD5sum: ac2f42f35332964a790fbc70973f6662 Package: EpiMix Version: 1.6.1 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: fc6639a1a0b36fa450474ebd5c12c086 Package: epimutacions Version: 1.8.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE MD5sum: 62358cc62245ac8e7a79991cc798920a Package: epiNEM Version: 1.28.0 Depends: R (>= 4.1) Imports: BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 MD5sum: bc63d75ebc805e3b942df8cf65796ac8 Package: epiregulon.extra Version: 1.0.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, lifecycle, patchwork, reshape2, scales, scater, stats Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE MD5sum: 5d1d10ca70be57180c9b5b8485fb7fe5 Package: epistack Version: 1.10.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: 036c437dd8f84c966f37a8317f64cf22 Package: epistasisGA Version: 1.6.0 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: 6065b236afc6588d4b659496253084eb Package: EpiTxDb Version: 1.16.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 7d777e5102aa0ebd4e60f39b5bf1228f Package: epivizr Version: 2.34.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: 106a82431e2e6e78550602d8a3e43bea Package: epivizrChart Version: 1.26.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: b3ef5f398b4c62d6615037ed5cd2995b Package: epivizrData Version: 1.32.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: d2f2d986fc025c0678d83a4a1439f138 Package: epivizrServer Version: 1.32.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: d4672167f86a7cea66d4223107a21af5 Package: epivizrStandalone Version: 1.32.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: 879e3a924f616f96ce73e94dda40717e Package: erccdashboard Version: 1.38.0 Depends: R (>= 3.2), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr License: GPL (>= 2) MD5sum: 80cc92d17a91ac940bc4248ebe1f0bb7 Package: erma Version: 1.20.0 Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2) Imports: rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel License: Artistic-2.0 MD5sum: e70c0e6843b1b8909bee934570e6a474 Package: ERSSA Version: 1.22.0 Depends: R (>= 4.0.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), apeglm (>= 1.4.2), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: f2428270728e79b39d132cbff5facc69 Package: escape Version: 2.0.0 Depends: R (>= 4.1) Imports: AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject Suggests: Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 88303f5d2dfb27a57bd98f01fd2876d0 Package: escheR Version: 1.4.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: 5e920041613e2d2d19f1600ab89cbd2a Package: esetVis Version: 1.30.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: b143918a2d9725e53ff93c4dc6e852ac Package: eudysbiome Version: 1.34.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: 3cf90beeebab0513362c7bcf9840c16c Package: evaluomeR Version: 1.20.5 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: 8bd16c92e76bdd7666e80f39f878c12d Package: EventPointer Version: 3.12.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: 7af2318c6b2a5916201a14d65cb1c4e1 Package: EWCE Version: 1.12.0 Depends: R (>= 4.2), RNOmni (>= 1.0) Imports: stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene (>= 0.99.8), data.table Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork License: GPL-3 MD5sum: 2d1d4043d393967c0d4affcc5d6658de Package: ExCluster Version: 1.22.0 Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges Imports: stats, methods, grDevices, graphics, utils License: GPL-3 MD5sum: 2fd466cffc48cc933376a79a8247fb7e Package: ExiMiR Version: 2.46.0 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) Suggests: mirna10cdf License: GPL-2 MD5sum: 17e54b2664b3e1d8f5595c1cc86ba774 Package: exomePeak2 Version: 1.16.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: Rsamtools,GenomicAlignments,GenomicRanges,GenomicFeatures,DESeq2,ggplot2,mclust,BSgenome,Biostrings,GenomeInfoDb,BiocParallel,IRanges,S4Vectors,rtracklayer,methods,stats,utils,BiocGenerics,magrittr,speedglm,splines Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: c3a906afa9ea293a883d8081b59914f4 Package: ExperimentHub Version: 2.12.0 Depends: methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.3.6), BiocFileCache (>= 1.5.1) Imports: utils, S4Vectors, BiocManager, rappdirs Suggests: knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments Enhances: ExperimentHubData License: Artistic-2.0 MD5sum: 82fe981c7628890e5b3d2b0a38b31d91 Package: ExperimentHubData Version: 1.30.0 Depends: utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData (>= 1.21.3) Imports: methods, ExperimentHub, BiocManager, DBI, httr, curl Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 37984a6a7712c760fde0fa108caa071e Package: ExperimentSubset Version: 1.14.0 Depends: R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment, SpatialExperiment, TreeSummarizedExperiment Imports: methods, Matrix, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway License: MIT + file LICENSE MD5sum: ecabdc4f0868da744b89763ad396ab47 Package: ExploreModelMatrix Version: 1.16.0 Imports: shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle License: MIT + file LICENSE MD5sum: ad973678056ee5f809cd5ee5bb411e28 Package: ExpressionAtlas Version: 1.32.0 Depends: R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 1d3e1f89a52ffd7203a82501e17f9f9f Package: extraChIPs Version: 1.8.1 Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.5.0), ggside (>= 0.3.1), SummarizedExperiment, tibble Imports: BiocIO, broom, ComplexUpset, csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb, GenomicInteractions, ggforce, ggrepel, glue, grDevices, grid, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram Suggests: BiocStyle, covr, cqn, DESeq2, EnrichedHeatmap, Gviz, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: c42511ea591a513a358bf1570ef61b3b Package: fabia Version: 2.50.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 1c31e5612ae595169eaf56c968be76a9 Package: factDesign Version: 1.80.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL MD5sum: e55183df86cc979095661fb8e2da8a54 Package: factR Version: 1.6.0 Depends: R (>= 4.2) Imports: BiocGenerics (>= 0.46), Biostrings (>= 2.68), GenomeInfoDb (>= 1.36), dplyr (>= 1.1), GenomicFeatures (>= 1.52), GenomicRanges (>= 1.52), IRanges (>= 2.34), purrr (>= 1.0), rtracklayer (>= 1.60), tidyr (>= 1.3), methods (>= 4.3), BiocParallel (>= 1.34), S4Vectors (>= 0.38), data.table (>= 1.14), rlang (>= 1.1), tibble (>= 3.2), wiggleplotr (>= 1.24), RCurl (>= 1.98), XML (>= 3.99), drawProteins (>= 1.20), ggplot2 (>= 3.4), stringr (>= 1.5), pbapply (>= 1.7), stats (>= 4.3), utils (>= 4.3), graphics (>= 4.3), crayon (>= 1.5) Suggests: AnnotationHub (>= 2.22), BSgenome (>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork License: file LICENSE MD5sum: acbea5f4896c422917b1dc7f8aec9db6 Package: faers Version: 1.0.0 Depends: R (>= 4.4.0) Imports: BiocParallel, brio, cli, curl (>= 5.0.0), data.table, httr2 (>= 1.0.0), MCMCpack, methods, openEBGM, rlang (>= 1.1.0), rvest, tools, utils, vroom, xml2 Suggests: BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: beb85140664b90c43e77d0a3c47f7329 Package: FamAgg Version: 1.32.0 Depends: methods, kinship2, igraph Imports: gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey Suggests: BiocStyle, knitr, RUnit, rmarkdown License: MIT + file LICENSE MD5sum: 2a57f8f2e3dbb96a0d49025de8268a92 Package: famat Version: 1.14.0 Depends: R (>= 4.0) Imports: KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2, rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex, tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager License: GPL-3 MD5sum: 2b5f0b1271b3b93b4b359f64c99e90ff Package: farms Version: 1.56.0 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) MD5sum: 58ed8f05e47f54b73ee91331b7cc6ef9 Package: fastLiquidAssociation Version: 1.40.0 Depends: methods, LiquidAssociation, parallel, doParallel, stats, Hmisc, utils Imports: WGCNA, impute, preprocessCore Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 MD5sum: d7c1c8e6581cd1bf41b81692ead6b86c Package: FastqCleaner Version: 1.22.0 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 83aa92dbc56bc20107505fd118b25a7e Package: fastreeR Version: 1.8.0 Depends: R (>= 4.4) Imports: ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 588a24cb5c7a8eb19e7bc7967e1502ba Package: fastseg Version: 1.50.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: methods, graphics, grDevices, stats, BiocGenerics, S4Vectors, IRanges Suggests: DNAcopy, oligo, BiocStyle, knitr License: LGPL (>= 2.0) MD5sum: e1626e2dd005b06d66d6dbd307e3a899 Package: FCBF Version: 2.12.0 Depends: R (>= 4.1) Imports: ggplot2, gridExtra, pbapply, parallel, SummarizedExperiment, stats, mclust Suggests: caret, mlbench, SingleCellExperiment, knitr, rmarkdown, testthat, BiocManager License: MIT + file LICENSE MD5sum: 1bbd8097c74d8f3c6f3d854dd949dfc7 Package: fCCAC Version: 1.30.0 Depends: R (>= 4.2.0), S4Vectors, IRanges, GenomicRanges, grid Imports: fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap, grDevices, stats, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 60bc80f248d4ed28071b008c37b498cd Package: fCI Version: 1.34.0 Depends: R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 0ba892b74f8a17680c6f50096478321b Package: fcScan Version: 1.18.0 Imports: stats, plyr, VariantAnnotation, SummarizedExperiment, rtracklayer, GenomicRanges, methods, IRanges, foreach, doParallel, parallel Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 5998cb6d727bf46f3cb7d568879404cc Package: fdrame Version: 1.76.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: 1537fcd59ca454071fb515e65da3656e Package: FEAST Version: 1.12.0 Depends: R (>= 4.1), mclust, BiocParallel, SummarizedExperiment Imports: SingleCellExperiment, methods, stats, utils, irlba, TSCAN, SC3, matrixStats Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: ab7a8a5b850ec53c55998d2f9c20fc90 Package: FeatSeekR Version: 1.4.0 Imports: pheatmap, MASS, pracma, stats, SummarizedExperiment, methods Suggests: rmarkdown, knitr, BiocStyle, DmelSGI, testthat (>= 3.0.0) License: GPL-3 MD5sum: 56771b4d57ccfe0074aed8a9141fac72 Package: fedup Version: 1.12.0 Depends: R (>= 4.1) Imports: openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer, RCy3, utils, stats Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr License: MIT + file LICENSE MD5sum: 196bad69a674b4ac5b0f522c9d361808 Package: FELLA Version: 1.24.0 Depends: R (>= 3.5.0) Imports: methods, igraph, Matrix, KEGGREST, plyr, stats, graphics, utils Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 MD5sum: 14757f024130c7bdfc2a7c39f7f62131 Package: fenr Version: 1.2.1 Depends: R (>= 4.1.0) Imports: tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect, tibble, purrr, readr, stringr, httr2, rvest, progress, BiocFileCache, shiny, ggplot2 Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO License: MIT + file LICENSE MD5sum: a71678ae4a19bea0866730efb8831a2a Package: ffpe Version: 1.48.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: 0990f70d6f62a3a15a7e47e7b66464fa Package: fgga Version: 1.12.0 Depends: R (>= 4.3), RBGL Imports: graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache, curl, igraph Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, BiocStyle License: GPL-3 MD5sum: 36a7c3c2e6210d87cec51c5a48f4bfc5 Package: FGNet Version: 3.38.0 Depends: R (>= 4.2.0) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager License: GPL (>= 2) MD5sum: d1605275c2ef6eae5781bf7f252f7bc5 Package: fgsea Version: 1.30.0 Depends: R (>= 4.1) Imports: Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, scales, utils LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat License: MIT + file LICENCE MD5sum: 4aac6bc844146df95dc7c1bdd7e4c759 Package: FilterFFPE Version: 1.14.0 Imports: foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors Suggests: BiocStyle License: LGPL-3 MD5sum: 660ab36509830937e4c85fb64e9a2f5d Package: findIPs Version: 1.0.0 Depends: graphics, R (>= 4.4.0) Imports: Biobase, BiocParallel, parallel, stats, SummarizedExperiment, survival, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: c5cc151e5384efcc5e6a94a8d4e9384d Package: FindIT2 Version: 1.10.0 Depends: GenomicRanges, R (>= 3.5.0) Imports: withr, BiocGenerics, GenomeInfoDb, rtracklayer, S4Vectors, GenomicFeatures, dplyr, rlang, patchwork, ggplot2, BiocParallel, qvalue, stringr, utils, stats, ggrepel, tibble, tidyr, SummarizedExperiment, MultiAssayExperiment, IRanges, progress, purrr, glmnet, methods Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 License: Artistic-2.0 MD5sum: 2a30392b3156688677321df7957b099b Package: FISHalyseR Version: 1.38.0 Depends: EBImage,abind Suggests: knitr License: Artistic-2.0 MD5sum: df06ac59ca08f9452a30c7540622104f Package: fishpond Version: 2.10.0 Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table License: GPL-2 MD5sum: bf754262dd4fba219abbeb956a49ed6e Package: FitHiC Version: 1.30.0 Imports: data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 296603867802d3bb2aab942fdc265e45 Package: flowAI Version: 1.34.0 Depends: R (>= 3.6) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny, BiocStyle License: GPL (>= 2) MD5sum: d51d4cf46a00a3c1530ca35592320127 Package: flowBeads Version: 1.42.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: 2e740909a8e911bce73338657bab6119 Package: flowBin Version: 1.40.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 MD5sum: a8dcce2c6ba9600e4d90af86dfe0c8c3 Package: flowcatchR Version: 1.38.0 Depends: R (>= 2.10), methods, EBImage Imports: colorRamps, abind, BiocParallel, graphics, stats, utils, plotly, shiny Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: c4ab01b712d1376e4fdaf71eb9d10289 Package: flowCHIC Version: 1.38.0 Depends: R (>= 3.1.0) Imports: methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid License: GPL-2 MD5sum: 527809d03129c0ebc952834e414edb22 Package: flowClean Version: 1.42.0 Depends: R (>= 2.15.0), flowCore Imports: bit, changepoint, sfsmisc Suggests: flowViz, grid, gridExtra License: Artistic-2.0 MD5sum: b3a7b12ac2d6f847ed25d207b07f82b7 Package: flowClust Version: 3.42.0 Depends: R(>= 2.5.0) Imports: BiocGenerics, methods, Biobase, graph, flowCore, parallel Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto, flowStats(>= 4.7.1) License: MIT MD5sum: 68533e6a5646c8dd9cc36951cdf9fb80 Package: flowCore Version: 2.16.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics, methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>= 2.13.1), S4Vectors LinkingTo: cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra License: Artistic-2.0 MD5sum: b1fcf9fd3fb81427f94709af6f76576c Package: flowCut Version: 1.14.0 Depends: R (>= 3.4), flowCore Imports: flowDensity (>= 1.13.1), Cairo, e1071, grDevices, graphics, stats,methods Suggests: RUnit, BiocGenerics, knitr, markdown, rmarkdown License: Artistic-2.0 MD5sum: 9ca2804e5d12c24655db21f4469c5758 Package: flowCyBar Version: 1.40.0 Depends: R (>= 3.0.0) Imports: gplots, vegan, methods License: GPL-2 MD5sum: db60ac3253a29173f5b9d1ae5d160028 Package: flowDensity Version: 1.38.0 Imports: flowCore, graphics, flowViz (>= 1.42), car, polyclip, gplots, methods, stats, grDevices Suggests: knitr,rmarkdown License: Artistic-2.0 MD5sum: 7833e3eff50ff26db34c9d2051843d9a Package: flowFP Version: 1.62.0 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 MD5sum: 4a91e6041fe42ab8fd242584586515fe Package: flowGate Version: 1.4.0 Depends: flowWorkspace (>= 4.0.6), ggcyto (>= 1.16.0), R (>= 4.2) Imports: shiny (>= 1.5.0), BiocManager (>= 1.30.10), flowCore (>= 2.0.1), dplyr (>= 1.0.0), ggplot2 (>= 3.3.2), rlang (>= 0.4.7), purrr, tibble, methods Suggests: knitr, rmarkdown, stringr, tidyverse, testthat License: MIT + file LICENSE MD5sum: 4f52b29653047d93b587e6ff9eb8fef3 Package: flowGraph Version: 1.12.0 Depends: R (>= 4.1) Imports: effsize, furrr, future, purrr, ggiraph, ggrepel, ggplot2, igraph, Matrix, matrixStats, stats, utils, visNetwork, htmlwidgets, grDevices, methods, stringr, stringi, Rdpack, data.table (>= 1.9.5), gridExtra, Suggests: BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: 924b0dd0d9c5713b1df0e9f0a9ebc320 Package: flowMap Version: 1.42.0 Depends: R (>= 3.0.1), ade4(>= 1.5-2), doParallel(>= 1.0.3), abind(>= 1.4.0), reshape2(>= 1.2.2), scales(>= 0.2.3), Matrix(>= 1.1-4), methods (>= 2.14) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 27e154e4b34ce466b2d3f6476bd30476 Package: flowMatch Version: 1.40.0 Depends: R (>= 3.0.0), Rcpp (>= 0.11.0), methods, flowCore Imports: Biobase LinkingTo: Rcpp Suggests: healthyFlowData License: Artistic-2.0 MD5sum: 4a6e68a9173c9321424b637f96c5d128 Package: flowMeans Version: 1.64.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 MD5sum: 354bbb89e52932f8056ce4e653e3d574 Package: flowMerge Version: 2.52.0 Depends: graph,feature,flowClust,Rgraphviz,foreach,snow Imports: rrcov,flowCore, graphics, methods, stats, utils Suggests: knitr, rmarkdown Enhances: doMC, multicore License: Artistic-2.0 MD5sum: 73c2d3fe0e962ade44a16f7b56fb40aa Package: flowPeaks Version: 1.50.0 Depends: R (>= 2.12.0) Suggests: flowCore License: Artistic-1.0 MD5sum: 90eb78ef4c892a846508675264349b3d Package: flowPloidy Version: 1.30.0 Imports: flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny, methods, graphics, stats, utils Suggests: flowPloidyData, testthat License: GPL-3 MD5sum: d7219ddaca0441aca8f87b285db33eb4 Package: flowPlots Version: 1.52.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 MD5sum: 92fb9fd127d7ea935b854a00c84648eb Package: FlowSOM Version: 2.12.0 Depends: R (>= 4.0), igraph Imports: stats, utils, colorRamps, ConsensusClusterPlus, dplyr, flowCore, ggforce, ggnewscale, ggplot2, ggpubr, grDevices, magrittr, methods, rlang, Rtsne, tidyr, BiocGenerics, XML Suggests: BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity License: GPL (>= 2) MD5sum: 4873ab407a90ea11f65fe23ddc52f02e Package: flowSpecs Version: 1.18.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), BiocGenerics (>= 0.30.0), BiocParallel (>= 1.18.1), Biobase (>= 2.48.0), reshape2 (>= 1.4.3), flowCore (>= 1.50.0), zoo (>= 1.8.6), stats (>= 3.6.0), methods (>= 3.6.0) Suggests: testthat, knitr, rmarkdown, BiocStyle, DepecheR License: MIT + file LICENSE MD5sum: e8f4a0210cf439213d5cf8d521842a66 Package: flowStats Version: 4.16.0 Depends: R (>= 3.0.2) Imports: BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace, ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, cluster, utils, KernSmooth, lattice, ks, RColorBrewer, rrcov, corpcor, mnormt, clue Suggests: xtable, testthat, openCyto, ggcyto, ggridges Enhances: RBGL,graph License: Artistic-2.0 MD5sum: f7c13e29cc719ac1b57771a20e228a3b Package: flowTime Version: 1.28.0 Depends: R (>= 3.4), flowCore Imports: utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto License: Artistic-2.0 MD5sum: f117abb5f88645e31276ead1827312e7 Package: flowTrans Version: 1.56.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: 276aa958350b7855a2613ec98a2d9f71 Package: flowViz Version: 1.68.0 Depends: R (>= 2.7.0), flowCore(>= 1.41.9), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace, flowStats, knitr, rmarkdown, markdown, testthat License: Artistic-2.0 MD5sum: fdbc68f7e37e34ceb1f75c96a0514b47 Package: flowVS Version: 1.36.0 Depends: R (>= 3.2), methods, flowCore, flowViz, flowStats Suggests: knitr, vsn, License: Artistic-2.0 MD5sum: 57bad1d5d2127cd7d6e6fb8eca83d52f Package: flowWorkspace Version: 4.16.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics, cytolib (>= 2.13.1), XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, scales(>= 1.3.0), matrixStats, RProtoBufLib, flowCore(>= 2.1.1), ncdfFlow(>= 2.25.4), DelayedArray, S4Vectors LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.3.7),Rhdf5lib Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto License_restricts_use: no MD5sum: 231e87769ce419d8fa19a5b7d78ee81b Package: fmcsR Version: 1.46.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown License: Artistic-2.0 MD5sum: 4707d12bd9d16d23045b4ea39f6a717a Package: fmrs Version: 1.14.0 Depends: R (>= 4.3.0) Imports: methods, survival, stats Suggests: BiocGenerics, testthat, knitr, utils License: GPL-3 MD5sum: e0bece343df6a3a09eb7654fee40160b Package: fobitools Version: 1.12.0 Depends: R (>= 4.1) Imports: clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr, ontologyIndex, purrr, RecordLinkage, stringr, textclean, tictoc, tidygraph, tidyr, vroom Suggests: BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse License: GPL-3 MD5sum: 6420a049622b116a1d96880b578c6e8a Package: FoldGO Version: 1.22.0 Depends: R (>= 4.0) Imports: topGO (>= 2.30.1), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), stats, methods Suggests: knitr, rmarkdown, devtools, kableExtra License: GPL-3 MD5sum: 1c2e10c9a920066b0ac2494db38707eb Package: FRASER Version: 2.0.0 Depends: BiocParallel, data.table, Rsamtools, SummarizedExperiment Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, DelayedArray (>= 0.5.11), DelayedMatrixStats, extraDistr, generics, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods, OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM LinkingTo: RcppArmadillo, Rcpp Suggests: magick, BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, rtracklayer, SGSeq, ggbio, biovizBase License: MIT + file LICENSE MD5sum: b6c7770a18a2da27a7f9a05ea62fd913 Package: frenchFISH Version: 1.16.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 78b715cd83896acfe2cd6bd71fadb8f6 Package: FRGEpistasis Version: 1.40.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: 415a99f914d6b9355a341f4710378c32 Package: frma Version: 1.56.0 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) MD5sum: 78824c87bd7c1be4a4854d6447df6a59 Package: frmaTools Version: 1.56.0 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) MD5sum: cf9c896f7c9d6dbb324377da89a76529 Package: FScanR Version: 1.14.0 Depends: R (>= 4.0) Imports: stats Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 33897d08cd902a9a75cf48d1e64f686e Package: FunChIP Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges Imports: shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer LinkingTo: Rcpp License: Artistic-2.0 MD5sum: 2cf1616a018ec6ec4f49f1a94caa2a40 Package: funtooNorm Version: 1.28.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: 7e02dafd5a39a3717b943a28f67cc34e Package: FuseSOM Version: 1.6.0 Depends: R (>= 4.2.0) Imports: psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster, fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest, methods, SummarizedExperiment, stats, S4Vectors LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: 5b7cf20b41ee9dab8f7705905da84f19 Package: GA4GHclient Version: 1.28.0 Depends: R (>= 3.5.0), S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: fac7a8361d450ba22416ba2646018ba6 Package: GA4GHshiny Version: 1.26.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 8163b574fef30a4da75c1fcd6a390703 Package: gaga Version: 2.50.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: 5d2664d5efe4b72f8316347b85f2f0c2 Package: gage Version: 2.54.0 Depends: R (>= 3.5.0) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: ce718c8bfbcf69cc798e370463f1be39 Package: GAprediction Version: 1.30.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 78649d4bb66daeeee32fb70bc3b4375e Package: garfield Version: 1.32.0 Suggests: knitr License: GPL-3 MD5sum: af9144f51a21d8ad5f7e577ee475822d Package: GARS Version: 1.24.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 32987720626d6587cd219bccfb90e64b Package: GateFinder Version: 1.24.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 5570e8115bdba086e1decc5afd6b871a Package: gatom Version: 1.2.0 Depends: R (>= 4.3.0) Imports: data.table, igraph, BioNet, plyr, methods, XML, sna, intergraph, network, GGally, grid, ggplot2, mwcsr, pryr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0) Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils License: MIT + file LICENCE MD5sum: 48a7951133d166c6319e379fd2bbb451 Package: GBScleanR Version: 1.8.18 Depends: SeqArray Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: dd8c1cd0e18ff2d9bce4973ed0f0ede9 Package: gcapc Version: 1.28.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: bbc1b977a1a5c8fc102e857c111b3d20 Package: gcatest Version: 2.4.0 Depends: R (>= 4.0) Imports: methods, lfa Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: 9a30e399bc9e57f31c1fd6828dd6fda0 Package: gCrisprTools Version: 2.10.0 Depends: R (>= 4.1) Imports: Biobase, limma, RobustRankAggreg, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea License: Artistic-2.0 MD5sum: bdb2baf92a1de9a8f5c5fe1c137e8a68 Package: gcrma Version: 2.76.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: f07b8f6580d170b378e4b1b00f01a251 Package: GDCRNATools Version: 1.24.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat, prettydoc, rmarkdown License: Artistic-2.0 MD5sum: 724b41c79874e589ec9d2d2c3c78e857 Package: gDNAx Version: 1.2.0 Depends: R (>= 4.3) Imports: methods, BiocGenerics, BiocParallel, matrixStats, Biostrings, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, GenomicFiles, GenomicAlignments, GenomicFeatures, Rsamtools, AnnotationHub, RColorBrewer, AnnotationDbi, bitops, plotrix, SummarizedExperiment, grDevices, graphics, stats, utils, cli Suggests: BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData License: Artistic-2.0 MD5sum: 757462a0f8f72c58e79dc4cb419d8d6a Package: gDR Version: 1.2.0 Depends: R (>= 4.2), gDRcore (>= 1.1.11), gDRimport (>= 1.1.4), gDRutils (>= 1.1.5) Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.1.3), gDRtestData (>= 1.1.7), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: ca403a041232ece821de65cb83a67c32 Package: gDRcore Version: 1.2.0 Depends: R (>= 4.2) Imports: BumpyMatrix, BiocParallel, checkmate, futile.logger, gDRutils (>= 1.1.3), MultiAssayExperiment, purrr, stringr, S4Vectors, SummarizedExperiment, data.table Suggests: BiocStyle, gDRstyle (>= 1.1.2), gDRimport (>= 1.1.4), gDRtestData (>= 1.1.6), IRanges, knitr, pkgbuild, qs, testthat, yaml License: Artistic-2.0 MD5sum: d11b56264384d27661c53c32bf1d2df7 Package: gDRimport Version: 1.2.0 Depends: R (>= 4.2) Imports: assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx, data.table, futile.logger, gDRutils (>= 1.1.5), magrittr, methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats, stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml, openxlsx Suggests: BiocStyle, gDRtestData (>= 1.1.7), gDRstyle (>= 1.1.3), knitr, purrr, qs, testthat License: Artistic-2.0 MD5sum: 59faa4d9ea37caa871097daee5c789c7 Package: gDRstyle Version: 1.2.0 Depends: R (>= 4.2) Imports: BiocCheck, BiocManager, checkmate, desc, git2r, lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild, withr Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f780d10c43d23bf9678a3578713fdc57 Package: gDRutils Version: 1.2.0 Depends: R (>= 4.2) Imports: BiocParallel, BumpyMatrix, checkmate, data.table, drc, jsonlite, jsonvalidate, methods, MultiAssayExperiment, S4Vectors, stats, stringr, SummarizedExperiment Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.1.5), gDRtestData (>= 1.1.10), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, testthat, tools, yaml License: Artistic-2.0 MD5sum: 95499045daef6b877308a0a0aaa17581 Package: GDSArray Version: 1.24.2 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: efffac77e0e71f596d6f35f8e4ba1b86 Package: gdsfmt Version: 1.40.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: 7d9bd111a7beb168e4879c6f1aefb207 Package: GeDi Version: 1.0.1 Depends: R (>= 4.4.0) Imports: GOSemSim, Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders, fontawesome, grDevices, parallel, stats, ggplot2, plotly, GeneTonic, RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools, BiocParallel, BiocFileCache Suggests: knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, htmltools, pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 0152faadc267e3311ccd32119dfafaf1 Package: GEM Version: 1.30.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: da1fdebaf873901933b7a43730adc4d1 Package: gemini Version: 1.18.0 Depends: R (>= 4.1.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: d6d264592a1ab857d86b188ed4228add Package: gemma.R Version: 3.0.8 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, base64enc Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, kableExtra, listviewer, shiny License: Apache License (>= 2) MD5sum: a04d139f795facf71be20b9b127ebfd8 Package: genArise Version: 1.80.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 3bbe0f742fec5f94af6f63c797c1b6b8 Package: geneAttribution Version: 1.30.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 5fad959ff04c7d645bb8c611718c88c3 Package: GeneBreak Version: 1.34.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: e67ef8c8a239e5d519c6f881c284d33b Package: geneClassifiers Version: 1.28.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: a03546e5c5c7f99b8432c259c7d8b5ce Package: GeneExpressionSignature Version: 1.50.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: a12865e96a2200e38a5fc55d323ef5bf Package: genefilter Version: 1.86.0 Imports: MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: a608f47d800427cc9279a3ec3e0360ce Package: genefu Version: 2.36.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: 07f02f3ca7cf07ab4d99ae280a04efad Package: GeneGA Version: 1.54.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 1b679869a74096d28aff486dda7d1d2d Package: GeneGeneInteR Version: 1.30.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 295cee59af95dcea6fc637871bab6708 Package: GeneMeta Version: 1.76.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: ffef268053b44895d0cd6a75c11e9e5f Package: GeneNetworkBuilder Version: 1.46.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: e6dd2b03bd39f2f7f5120bd0b27ddf8f Package: GeneOverlap Version: 1.40.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: ef145cb43de62e955d260639f911b8f9 Package: geneplast Version: 1.30.0 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: e2c4b28decbe82a11a6f351f635309fd Package: geneplotter Version: 1.82.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr License: Artistic-2.0 MD5sum: 8db031468eb3c17e9bc1b54f3c700711 Package: geneRecommender Version: 1.76.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 9f98435382b389e5f96670e10dd0c476 Package: GeneRegionScan Version: 1.60.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 66cc6053daef512fca36d468864ad735 Package: geneRxCluster Version: 1.40.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 93b9981701c467efbc5685d9972a3ac5 Package: GeneSelectMMD Version: 2.48.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: cf7989229e837565c2dedff47cb9833f Package: GENESIS Version: 2.34.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 72e8ad2e9e68a2b4ec09affd590f4fee Package: GeneStructureTools Version: 1.24.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 488c0b58180b405ba195e70d74cf6345 Package: geNetClassifier Version: 1.44.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 84fc644872f851f12776cdb09f089e95 Package: GeneticsPed Version: 1.66.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: acaf2ef342fcd8f62ac4915e6e758204 Package: GeneTonic Version: 2.8.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: bd060645af171dc374a54b7938089df8 Package: geneXtendeR Version: 1.30.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) MD5sum: 0fbe3f9e98e4f06a6fc1f0c106d5d0bb Package: GENIE3 Version: 1.26.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: 07af1d04dcb03cc6e0ff3197c143700e Package: genoCN Version: 1.56.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 5af1e4bf04719a6035cb08ee2349b233 Package: genomation Version: 1.36.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 7d0b56f858c48edf65f3420c4ad4c350 Package: GenomeInfoDb Version: 1.40.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, UCSC.utils, GenomeInfoDbData Suggests: R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: d8b8110daba9170d8a0c93fa339dfbb8 Package: genomeIntervals Version: 1.60.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 738f48ccc940b4d82317902859a88d3a Package: genomes Version: 3.34.0 Depends: readr, curl License: GPL-3 MD5sum: c7e6139db534a7d43f3774e704fb127d Package: GenomicAlignments Version: 1.40.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.55.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: d8ec2747b3f02db8384558934cce897a Package: GenomicDataCommons Version: 1.28.0 Depends: R (>= 3.4.0), magrittr Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: c7a5c6a300ece227f6cf1c172e396bd1 Package: GenomicDistributions Version: 1.12.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: f6317846398616e1f9447044da1ff8c2 Package: GenomicFeatures Version: 1.56.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.37.1), GenomeInfoDb (>= 1.35.8), GenomicRanges (>= 1.55.2), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings, rtracklayer Suggests: txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 5b484458ef92ef89cd5f211ee508a57f Package: GenomicFiles Version: 1.40.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: 45e57e0ad3d7b157d84dfbd9fccc976f Package: genomicInstability Version: 1.10.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: dca4da36ad0c44e6dd6b74684dbee3c2 Package: GenomicInteractionNodes Version: 1.8.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: 98641a532c56d5348834f2d19c9b527a Package: GenomicInteractions Version: 1.38.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 9705a50d8b0d11d4fec9cf99b235a88e Package: GenomicOZone Version: 1.18.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 74baf00ad1e5f1c16e27320390487337 Package: GenomicPlot Version: 1.2.3 Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, GenomeInfoDb, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr, grDevices, graphics, stats, utils, GenomicFeatures, genomation (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi License: GPL-2 MD5sum: daef1cbb433fbf40ba78d380ddbb92fe Package: GenomicRanges Version: 1.56.1 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.37.1), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 6d6f7496cbab507998e0d4998a191ef7 Package: GenomicScores Version: 2.16.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: c0d442f335bf8dcec11ab72303aaaa27 Package: GenomicSuperSignature Version: 1.12.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: 0dd47cfee9eb015c29c15042df5314a3 Package: GenomicTuples Version: 1.38.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings License: Artistic-2.0 MD5sum: 564f3ae4a18338c38f1275c835a67727 Package: GenProSeq Version: 1.8.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: d20455005f71f69d24535ce928c43daf Package: GenVisR Version: 1.36.0 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: a93322042310c67f2653da65f88778d1 Package: GeoDiff Version: 1.10.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 971a232debaff970e2c218d5c9d584fc Package: GEOexplorer Version: 1.10.0 Depends: shiny, limma, Biobase, plotly, enrichR, R (>= 4.1.0) Imports: DT, XML, httr, sva, xfun, edgeR, htmltools, factoextra, heatmaply, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, markdown, knitr, utils, xml2, R.utils, readxl, shinycssloaders, car Suggests: rmarkdown, usethis, testthat (>= 3.0.0) License: GPL-3 MD5sum: 68f035a72beb8825aa07f38cc2cde97d Package: GEOfastq Version: 1.12.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 36a0e1b55e6f4c7db1425fa38f9126c4 Package: GEOmetadb Version: 1.66.0 Depends: GEOquery,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 67ee8009483b9f5c5982fe13a8de3685 Package: GeomxTools Version: 3.8.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: d817b685742d55cb86ed5bf7abceb05f Package: GEOquery Version: 2.72.0 Depends: methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, R.utils Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown License: MIT MD5sum: 2e6634c2b78cf251e22d610e81ba673c Package: GEOsubmission Version: 1.56.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: 70d7aac949caa22fe584f67a30e29212 Package: GeoTcgaData Version: 2.4.0 Depends: R (>= 4.2.0) Imports: utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics License: Artistic-2.0 MD5sum: c295fb3efe3c92234ae676c5e68828d0 Package: gep2pep Version: 1.24.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 754f3a005a77a1e6f7637446125a4e8c Package: gespeR Version: 1.36.0 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr Suggests: knitr License: GPL-3 MD5sum: e6a790085095be17ead04e8c2071043f Package: getDEE2 Version: 1.14.0 Depends: R (>= 4.0) Imports: stats, utils, SummarizedExperiment, htm2txt Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: 44e093cfa62569c156e0537363f6fdb8 Package: geva Version: 1.12.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 MD5sum: e552d54e8d27879e6f646f3d7f12c4c8 Package: GEWIST Version: 1.48.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: 2080ed2af7bc56d1802c094dec12fa79 Package: gg4way Version: 1.2.0 Depends: R (>= 4.3.0), ggplot2 Imports: DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr, methods, purrr, rlang, scales, stats, stringr, tibble, tidyr Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat License: MIT + file LICENSE MD5sum: ccd9a855a8d611b0ee36284db444a3b5 Package: ggbio Version: 1.52.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 18eefad1d1d7907e61f39d4e80d41049 Package: ggcyto Version: 1.32.0 Depends: methods, ggplot2(>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE MD5sum: 0504e4b8b0a78ed9fbe63826f440ec33 Package: ggkegg Version: 1.2.2 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, GetoptLong, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, org.Hs.eg.db, methods, utils, stats, AnnotationDbi, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 566c8de7a076ce1e9abd5049199b92b9 Package: ggmanh Version: 1.8.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), markdown, GenomicRanges License: MIT + file LICENSE MD5sum: 3f6dcbcf2a03809c9fd93b540e32b99d Package: ggmsa Version: 1.10.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e65961d4ddeb569a14b37bb4ffe428d4 Package: GGPA Version: 1.16.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 0bd347928a5c9979510e2dcc549703ba Package: ggsc Version: 1.2.0 Imports: Rcpp, RcppParallel, cli, dplyr, ggfun, ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie, scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 67668b9a92120fedae8d4d842d6a0bd4 Package: ggspavis Version: 1.10.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: 049f51b50eab2451713ece0d3b6f3e2b Package: ggtree Version: 3.12.0 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.0.9), yulab.utils, tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats, cli Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue License: Artistic-2.0 MD5sum: b090048cffd8db728c9c71fcd8466466 Package: ggtreeDendro Version: 1.6.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree, utils Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 MD5sum: bf1bc7a620276b11f3a7f681b116eb0f Package: ggtreeExtra Version: 1.14.0 Imports: ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) MD5sum: cf05f79bd78d21f6fe7586c14ddb0e53 Package: ggtreeSpace Version: 1.0.0 Imports: interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools, rlang, tibble, tidyr, tidyselect, stats Suggests: knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 312434c3fe5a1faeb7223fcbe0217531 Package: GIGSEA Version: 1.22.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 7f11f3d81ec5742a8f10f850f628a1f3 Package: ginmappeR Version: 1.0.2 Imports: KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise, cachem Suggests: RUnit, BiocGenerics, markdown, knitr License: GPL-3 + file LICENSE MD5sum: 18b7484fb10ec31d68dc55730c7bfa8d Package: gINTomics Version: 1.0.0 Depends: R (>= 4.4.0) Imports: BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges, gtools, MultiAssayExperiment, plyr, stringi, stringr, SummarizedExperiment, methods, stats, reshape2, randomForest, limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, GenomicFeatures, ReactomePA, clusterProfiler, dplyr, AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges, ggtree, shinydashboard, plotly, DT, MASS, InteractiveComplexHeatmap, ComplexHeatmap, visNetwork, shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr, circlize Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 398353e00e4b50e826e64c31af29b829 Package: girafe Version: 1.56.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), pwalign, graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 MD5sum: 1445625bd874b4bd71202f7b8c2930c6 Package: GLAD Version: 2.68.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 33f759c0557ef3c7ffa03bfbb0c9676b Package: GladiaTOX Version: 1.20.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 5a86522fae5f0caf8598e64237413da7 Package: Glimma Version: 2.14.0 Depends: R (>= 4.0.0) Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran License: GPL-3 MD5sum: 205195b1f389e423be0ec5a83da9d916 Package: glmGamPoi Version: 1.16.0 Imports: Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics, DelayedArray, HDF5Array, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs LinkingTo: Rcpp, RcppArmadillo, beachmat Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr License: GPL-3 MD5sum: 13fae29d90afb178b97943fb163d2cea Package: glmSparseNet Version: 1.22.0 Depends: R (>= 4.3.0) Imports: biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2, glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet, Matrix, MultiAssayExperiment, SummarizedExperiment, survminer, TCGAutils, utils Suggests: BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC, rmarkdown, survival, testthat, VennDiagram, withr License: GPL-3 MD5sum: d882e6d61164b2aace3e5bd5c8dd2bb0 Package: GlobalAncova Version: 4.22.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: dd3095292c0fd7ec1642b33a34da4eff Package: globalSeq Version: 1.32.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 3275229dd99f60cb444ac9099031e1ae Package: GloScope Version: 1.2.0 Depends: R (>= 4.3.0) Imports: utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter License: Artistic-2.0 MD5sum: 21ef2e6ac91010c87548584830482162 Package: gmapR Version: 1.46.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: ad94ffc38e52976785ce66f3ebe4872d Package: GmicR Version: 1.18.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: f0f1bd3370a03132d9e0fbcad1c52f57 Package: gmoviz Version: 1.16.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 MD5sum: a091c08353c935ce795db104bdce3865 Package: GMRP Version: 1.32.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: c7fec09ea09aded8f4de2964e78ff3ad Package: GNET2 Version: 1.20.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 2d30ff4d641beccb98f73ece008c1bf2 Package: GNOSIS Version: 1.2.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 2db2b1a2feffdcf351182be632d22f33 Package: GOexpress Version: 1.38.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: ed90436b47309312229604a93eaddce7 Package: GOfuncR Version: 1.24.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: 168c67c04427beb90a51ca06f3d4c6e4 Package: GOpro Version: 1.30.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: e75a6a1a20d476a8bec1a387a89f26de Package: goProfiles Version: 1.66.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: c508dbdfd472bc8561f9bfa2c2b8553a Package: GOSemSim Version: 2.30.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, GO.db, methods, rlang, stats, utils, yulab.utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 30b579b7bdd198b1d67f8dd38c9e22bb Package: goseq Version: 1.56.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db,BiocGenerics Suggests: edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) MD5sum: 7e37fbcdcaae5ac1be543ab66c2e585c Package: GOSim Version: 1.42.0 Depends: GO.db, annotate Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp LinkingTo: Rcpp Enhances: igraph License: GPL (>= 2) MD5sum: 98925a716b31fb318f4812ea56661180 Package: goSorensen Version: 1.6.0 Depends: R (>= 4.3.0) Imports: GO.db, org.Hs.eg.db, goProfiles, stats, clusterProfiler, parallel, stringr Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 62ac224455995f90b52f294f3d9aa821 Package: goSTAG Version: 1.28.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: dc99ccc121ad2f4523dbc06d95b5dcf5 Package: GOstats Version: 2.70.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 7d47c865e53a104aaf355260b7578c88 Package: GOTHiC Version: 1.40.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: a39b2b60b998a3f2eb5c9b9b4edc705a Package: goTools Version: 1.78.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: 4e4f9a1409b7c9ce343c5b28ab68479a Package: GPA Version: 1.16.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: ee72da7fa784154814b6717f33d8b503 Package: gpls Version: 1.76.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 6bdda1126285e681d81dbdd0ad68f14a Package: GrafGen Version: 1.0.0 Depends: R (>= 4.3.0) Imports: stats, utils, graphics, ggplot2, plotly, zlibbioc, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools License: GPL-2 MD5sum: d2da79bc9882d2f362da78d78180b093 Package: GRaNIE Version: 1.8.0 Depends: R (>= 4.2.0) Imports: futile.logger, checkmate, patchwork, reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr, dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024, TFBSTools, motifmatchr, rbioapi, LDlinkR License: Artistic-2.0 MD5sum: f70cb2113a92632b177cb40e1eca2bd0 Package: granulator Version: 1.12.0 Depends: R (>= 4.1) Imports: cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify, grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap, purrr, rlang, stats, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: b383e13f9858674c27171a7acb904fb0 Package: graper Version: 1.20.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: e4b08563636cdd0e1fb10a91e2cea5c3 Package: graph Version: 1.82.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 MD5sum: a5e97ec6b7ca5c568a88a10b0a51dbeb Package: GraphAlignment Version: 1.68.0 License: file LICENSE License_restricts_use: yes MD5sum: 9657103f42fab86c654118cc21362694 Package: GraphAT Version: 1.76.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: c7ac59edb13161d6a9fb2262c20f1213 Package: graphite Version: 1.50.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: 1c06caecd75382f94739bd04cb18b172 Package: GraphPAC Version: 1.46.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 2653340401bdb56dd985055c22eee6a7 Package: GRENITS Version: 1.56.0 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) MD5sum: 393cf7fc97e3b673d7d8819c972493ee Package: GreyListChIP Version: 1.36.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 7f739b1a486c20dc69106e3e47d10c30 Package: GRmetrics Version: 1.30.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 MD5sum: a4e5a96aa79dd87be786d6aa966cfb4f Package: groHMM Version: 1.38.0 Depends: R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 769709411a0840fee9e7a95f4a09e8bc Package: GSALightning Version: 1.32.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 229090f45e2f5da3425b78b01b4897db Package: GSAR Version: 1.38.0 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: a3b4610e60205da9d38c075575a35998 Package: GSCA Version: 2.34.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: 26921c0b2e3accda7e427629e7f012a5 Package: gscreend Version: 1.18.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: 523c66c1da7bd23c4c22237d11cc90f3 Package: GSEABase Version: 1.66.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit License: Artistic-2.0 MD5sum: 1e586b3bd328488d504ad204045a0f7b Package: GSEABenchmarkeR Version: 1.24.0 Depends: R (>= 3.5.0), Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 MD5sum: 886ff976d965b4a0e211b120fa392f2c Package: GSEAlm Version: 1.64.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 3264f5eaafcfde75c0c5e483d173ebff Package: GSEAmining Version: 1.14.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm License: GPL-3 | file LICENSE MD5sum: d42e68cf60b1d3b8c2ffc7b4df7ef684 Package: gsean Version: 1.24.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: 4aecde3262db0339a90248d2771790b6 Package: GSgalgoR Version: 1.14.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: efe0432766dca3154c47d953850e6c1b Package: GSReg Version: 1.38.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: b9a92fb61397826420aa71c6dfc6ce67 Package: GSRI Version: 2.52.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: 729a7c783a5616d8f799a466993b0661 Package: GSVA Version: 1.52.3 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, S4Vectors, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, BiocParallel, SingleCellExperiment, SpatialExperiment, sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array, BiocSingular Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) MD5sum: 55f18286a62577d3a2aa0c048b678509 Package: gtrellis Version: 1.36.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: 6d07bdf7956f8f351a94ed797acff735 Package: GUIDEseq Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 8027a1581b04d67c82c4b3bbd658d450 Package: Guitar Version: 2.20.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: b0bd79e972bd7a30f9caa10d09956c4b Package: Gviz Version: 1.48.0 Depends: R (>= 4.3), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), ensembldb (>= 2.11.3), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8), graphics, grDevices, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 63463bbf5ed5c88b94270d34111eb40e Package: GWAS.BAYES Version: 1.14.0 Depends: R (>= 4.3.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), limma (>= 3.54.0), stats (>= 4.2.2), MASS (>= 7.3-58.1) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP License: GPL-3 + file LICENSE MD5sum: 7004913fe32c9e55a68d75a63be9a45f Package: gwascat Version: 2.36.0 Depends: R (>= 3.5.0), methods Imports: S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: b3c1cd5ffc70ec129683e264e10590bb Package: GWASTools Version: 1.50.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr License: Artistic-2.0 MD5sum: 0009477ca499f31b44e8fb33b376df5d Package: gwasurvivr Version: 1.22.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: b1e21d3158a6f09d1f5d2005aeaf6b5c Package: GWENA Version: 1.14.0 Depends: R (>= 4.1) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1), ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5), tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment (>= 1.14.1), stringr (>= 1.4.0), cluster (>= 2.1.0), grDevices (>= 4.0.4), methods, graphics, stats, utils Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) License: GPL-3 MD5sum: e2db3c9b552ec05de77aefdf119e1ce3 Package: gypsum Version: 1.0.1 Imports: utils, tools, httr2, jsonlite, parallel, filelock Suggests: knitr, rmarkdown, testthat, BiocStyle, digest, jsonvalidate, DBI, RSQLite, S4Vectors, methods License: MIT + file LICENSE MD5sum: 22decdf190ebc70b06c9ec5d74e332aa Package: h5vc Version: 2.38.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>= 2.13.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb LinkingTo: Rhtslib (>= 1.99.1) Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown License: GPL (>= 3) MD5sum: 2cfda577c15bd59498c99cd95c046083 Package: hapFabia Version: 1.46.0 Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: bcbcd9ff84a231cf4c80695cc54ad047 Package: Harman Version: 1.32.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats LinkingTo: Rcpp Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE MD5sum: 9aeb924705d71977e44801228add0304 Package: HarmonizR Version: 1.2.0 Depends: R (>= 4.2.0) Imports: doParallel (>= 1.0.16), foreach (>= 1.5.1), janitor (>= 2.1.0), plyr (>= 1.8.6), sva (>= 3.36.0), seriation (>= 1.3.5), limma (>= 3.46.0), SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 298e487375cef1af6585d1f5b4dbbd37 Package: Harshlight Version: 1.76.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: 9b65d06f9bdf35a878994c62f7c78e26 Package: hca Version: 1.12.0 Depends: R (>= 4.1) Imports: httr, jsonlite, dplyr, tibble, tidyr, readr, BiocFileCache, tools, utils, digest, shiny, miniUI, DT Suggests: LoomExperiment, SummarizedExperiment, SingleCellExperiment, S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 660b86658ac7b9ed14ac04b301646eb9 Package: HDF5Array Version: 1.32.0 Depends: R (>= 3.4), methods, DelayedArray (>= 0.27.2), rhdf5 (>= 2.31.6) Imports: utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>= 0.31.5), S4Vectors, IRanges, S4Arrays (>= 1.1.1) LinkingTo: S4Vectors (>= 0.27.13), Rhdf5lib Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment, DelayedMatrixStats, genefilter License: Artistic-2.0 MD5sum: 7f140b7889390bb053f6841ad77417d0 Package: HDTD Version: 1.38.0 Depends: R (>= 4.1) Imports: stats, Rcpp (>= 1.0.1) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 60620500d6918cdc54296d53000fb58e Package: hdxmsqc Version: 1.0.1 Depends: R(>= 4.3), QFeatures, S4Vectors, Spectra Imports: dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices, stats, MsCoreUtils Suggests: RColorBrewer, pheatmap, MASS, patchwork, testthat License: file LICENSE MD5sum: 5d791a5d6ebe02cbf95914bf0ad0e8b6 Package: heatmaps Version: 1.28.0 Depends: R (>= 3.5.0) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, GenomeInfoDb Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: add87a27c2da81432c771ee99267f5e2 Package: Heatplus Version: 3.12.0 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: cc308fdc6e937ddab4e3a073eda58176 Package: HelloRanges Version: 1.30.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3), BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>= 1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer (>= 1.33.8), GenomeInfoDb, SummarizedExperiment, BiocIO Imports: docopt, stats, tools, utils Suggests: HelloRangesData, BiocStyle, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 040f1a775d01c0c077f6e72c55e21b93 Package: HELP Version: 1.62.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) MD5sum: 10383e9101653377e635b613f280703a Package: HEM Version: 1.76.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) MD5sum: 8c8274938a07be8f2c6b5e283b150cfb Package: hermes Version: 1.8.1 Depends: ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16) Imports: assertthat, Biobase, BiocGenerics, biomaRt, checkmate (>= 2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats, forcats (>= 1.0.0), GenomicRanges, ggplot2, ggrepel (>= 0.9), IRanges, lifecycle, limma, magrittr, matrixStats, methods, MultiAssayExperiment, purrr, R6, Rdpack, rlang, S4Vectors, stats, tidyr, utils Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr License: Apache License 2.0 MD5sum: a4225586a735a216feac4007f30bfc20 Package: HERON Version: 1.2.0 Depends: R (>= 4.3.0), SummarizedExperiment (>= 1.1.6), GenomicRanges, IRanges, S4Vectors Imports: matrixStats, stats, data.table, harmonicmeanp, metap, cluster, spdep, Matrix, limma, methods Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 992a4ce0987b2383eab70a3306786570 Package: HGC Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape, dendextend, ggplot2, mclust, patchwork, dplyr, grDevices, methods, stats LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: c4eed3d00ea1c5cf3cf2adff03d688d8 Package: hiAnnotator Version: 1.38.0 Depends: GenomicRanges, R (>= 2.10) Imports: foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales, methods Suggests: knitr, doParallel, testthat, BiocGenerics, markdown License: GPL (>= 2) MD5sum: bd3d06ef539a435d7ad0cf69b1ffa983 Package: HIBAG Version: 1.40.0 Depends: R (>= 3.2.0) Imports: methods, RcppParallel LinkingTo: RcppParallel (>= 5.0.0) Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown, Rsamtools License: GPL-3 MD5sum: ebe5c0ab3eabeeb7ad68f9a02af1df1c Package: HicAggR Version: 1.0.2 Depends: R (>= 4.2.0) Imports: InteractionSet, BiocGenerics, BiocParallel, dplyr, GenomeInfoDb, GenomicRanges, ggplot2, grDevices, IRanges, Matrix, methods, rhdf5, rlang, rtracklayer, S4Vectors, stats, utils, strawr, tibble, stringr, tidyr, gridExtra, data.table, reshape, checkmate, purrr, withr Suggests: covr, tools, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache (>= 2.6.1) License: MIT + file LICENSE MD5sum: 9cbea56976fd47531b00dbf13070a523 Package: HiCBricks Version: 1.22.0 Depends: R (>= 3.6), utils, curl, rhdf5, R6, grid Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 69203557c21c8f21a5de997b70efbdd5 Package: HiCcompare Version: 1.26.0 Depends: R (>= 3.5.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE MD5sum: 7b8a57bb2c390914d3ab3a0fa9ce28d1 Package: HiCDCPlus Version: 1.12.0 Imports: Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors LinkingTo: Rcpp Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 MD5sum: ea7bacfa0f0bc29e22f1ca6e41ab19d0 Package: HiCDOC Version: 1.6.0 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, GenomeInfoDb LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 License: LGPL-3 MD5sum: cbebf2880f5aa9123bcb4e81bcb9d015 Package: HiCExperiment Version: 1.4.0 Depends: R (>= 4.2) Imports: InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 47e479d5ef0801dd10eafdbf0643d924 Package: HiContacts Version: 1.6.0 Depends: R (>= 4.2), HiCExperiment Imports: InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 473ebee2040d5c8227c311c42635a539 Package: hicVennDiagram Version: 1.2.0 Depends: R (>= 4.3.0) Imports: GenomeInfoDb, GenomicRanges, IRanges, InteractionSet, rtracklayer, ggplot2, ComplexUpset, reshape2, eulerr, S4Vectors, methods, utils, htmlwidgets, svglite Suggests: BiocStyle, knitr, rmarkdown, testthat, ChIPpeakAnno, grid, TxDb.Hsapiens.UCSC.hg38.knownGene License: GPL-3 MD5sum: 98360a684cd4dee93ffd7bbfef2ad924 Package: hierGWAS Version: 1.34.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 MD5sum: a6352e2bcef5ddd79f076bef819695ab Package: hierinf Version: 1.22.0 Depends: R (>= 3.6.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE MD5sum: 84fc005869216d4a0cac3ac2cd655066 Package: HilbertCurve Version: 1.34.0 Depends: R (>= 3.6.0), grid Imports: methods, utils, HilbertVis, png, grDevices, circlize (>= 0.3.3), IRanges, GenomicRanges, polylabelr Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown License: MIT + file LICENSE MD5sum: 22e6545f064de5b1e20297c115ca217f Package: HilbertVis Version: 1.62.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) MD5sum: edd7daad5610f0a0720c37a7be2f7407 Package: HiLDA Version: 1.18.0 Depends: R(>= 4.1), ggplot2 Imports: R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges, S4Vectors, XVector, Biostrings, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: f28b69a3592a37909e4756feb1fea2f7 Package: hipathia Version: 3.4.0 Depends: R (>= 4.1), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5), MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1) Imports: coin, stats, limma, grDevices, utils, graphics, preprocessCore, servr, DelayedArray, matrixStats, methods, S4Vectors, ggplot2, ggpubr, dplyr, tibble, visNetwork, reshape2, MetBrewer Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: b8c08c4fff6be0d9c3e2db737af73548 Package: HIPPO Version: 1.16.0 Depends: R (>= 3.6.0) Imports: ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 5ffdb14dcaabeb449dbc1303606c39e3 Package: hiReadsProcessor Version: 1.40.0 Depends: R (>= 3.5.0), Biostrings, pwalign, GenomicAlignments, BiocParallel, hiAnnotator Imports: sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods Suggests: knitr, testthat, markdown License: GPL-3 MD5sum: 2dd489cf6c642d9d54f549e468d2192a Package: HIREewas Version: 1.22.0 Depends: R (>= 3.5.0) Imports: quadprog, gplots, grDevices, stats Suggests: BiocStyle, knitr, BiocGenerics License: GPL (>= 2) MD5sum: 38f846ec1a2400be793c623f0067ac17 Package: HiTC Version: 1.48.0 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix, parallel, GenomeInfoDb Suggests: BiocStyle, HiCDataHumanIMR90, BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 MD5sum: e9eca79ce82a2ed5aad79844d5cfe478 Package: hmdbQuery Version: 1.24.0 Depends: R (>= 3.5), XML Imports: S4Vectors, methods, utils Suggests: knitr, annotate, gwascat, testthat, rmarkdown License: Artistic-2.0 MD5sum: c7807f9c43cd0a7341408ae26550352b Package: HMMcopy Version: 1.46.0 Depends: R (>= 2.10.0), data.table (>= 1.11.8) License: GPL-3 MD5sum: f44ca962c34b9eb85bbffba9d1957565 Package: hoodscanR Version: 1.2.0 Depends: R (>= 4.3) Imports: knitr, rmarkdown, SpatialExperiment, SummarizedExperiment, circlize, ComplexHeatmap, scico, rlang, utils, ggplot2, grid, methods, stats, RANN, Rcpp (>= 1.0.9) LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-3 + file LICENSE MD5sum: 8e212e15c3b31539addcaef2ef9bc863 Package: hopach Version: 2.64.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: c1c40337e9ef1191e1b3d704b4edcbe0 Package: HPAanalyze Version: 1.22.0 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra Suggests: knitr, rmarkdown, markdown, devtools, BiocStyle License: GPL-3 + file LICENSE MD5sum: 3c80a43e89834bd47126cef45a29a379 Package: hpar Version: 1.46.0 Depends: R (>= 3.5.0) Imports: utils, ExperimentHub Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT License: Artistic-2.0 MD5sum: 1a9c04c78d167fb34df20fce3d44672a Package: HPiP Version: 1.10.0 Depends: R (>= 4.1) Imports: dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble, utils, stringr, magrittr, caret, corrplot, ggplot2, pROC, PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr License: MIT + file LICENSE MD5sum: d550fa71ee5605d1596e445e1f2d954d Package: HTSFilter Version: 1.44.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: ea957aa26768c1189f88aeba7b111740 Package: HubPub Version: 1.12.0 Imports: available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager, utils Suggests: AnnotationHubData, ExperimentHubData, testthat, knitr, rmarkdown, BiocStyle, License: Artistic-2.0 MD5sum: b226968afa5a7a120e1417f6875afa54 Package: HumanTranscriptomeCompendium Version: 1.20.0 Depends: R (>= 3.6) Imports: shiny, ssrch, S4Vectors, SummarizedExperiment, utils, BiocManager Suggests: knitr, BiocStyle, beeswarm, tximportData, DT, tximport, dplyr, magrittr, BiocFileCache, testthat, rhdf5client, rmarkdown License: Artistic-2.0 MD5sum: 269ed1dd19b68b3be3c6e59290cc9e2f Package: hummingbird Version: 1.14.0 Depends: R (>= 4.0) Imports: Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: d6e30f38c67afc8ed3a8489719be4e0d Package: HybridExpress Version: 1.0.0 Depends: R (>= 4.3.0) Imports: ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment, stats, methods, RColorBrewer, ComplexHeatmap, grDevices, BiocParallel Suggests: BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: 52bb4a43ad4abe56f4a2ae23da200d52 Package: HybridMTest Version: 1.48.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) MD5sum: 94634b7f7c21800d437f80936a59a807 Package: hypeR Version: 2.2.0 Depends: R (>= 3.6.0) Imports: ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr, scales, rlang, httr, openxlsx, htmltools, reshape2, reactable, msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny, BiocStyle Suggests: tidyverse, devtools, testthat, knitr License: GPL-3 + file LICENSE MD5sum: c51eea22fd696e29f4241e9398239725 Package: hyperdraw Version: 1.56.0 Depends: R (>= 2.9.0) Imports: methods, grid, graph, hypergraph, Rgraphviz, stats4 License: GPL (>= 2) MD5sum: dd307ce72176d9d77fc24f224dda882d Package: hypergraph Version: 1.76.0 Depends: R (>= 2.1.0), methods, utils, graph Suggests: BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 3b073d6fe420b3e5010a6faa8e7d8809 Package: iASeq Version: 1.48.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 MD5sum: 8379b7bed89aa6269805ad95a57a6c8e Package: iasva Version: 1.22.0 Depends: R (>= 3.5), Imports: irlba, stats, cluster, graphics, SummarizedExperiment, BiocParallel Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer License: GPL-2 MD5sum: c76006e0b50756a7767a1cbc6db9f63e Package: iBBiG Version: 1.48.0 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 MD5sum: c44acbfb9cd3ea56a13e15f44cfbc140 Package: ibh Version: 1.52.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) MD5sum: cc6d6c0a37d511af323937a4170e779f Package: iCARE Version: 1.32.0 Depends: R (>= 3.3.0), plotrix, gtools, Hmisc Suggests: RUnit, BiocGenerics License: GPL-3 + file LICENSE MD5sum: 2d4a33155b6b53d1ef64aa41f7923861 Package: Icens Version: 1.76.0 Depends: survival Imports: graphics License: Artistic-2.0 MD5sum: a3f4b6652403ac4803d5c7dbd2cd7c49 Package: icetea Version: 1.22.0 Depends: R (>= 4.0) Imports: stats, utils, methods, graphics, grDevices, ggplot2, GenomicFeatures, ShortRead, BiocParallel, Biostrings, S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, DESeq2, TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: d9ef23af7884bab42efa3c12ec409f3c Package: iCheck Version: 1.34.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: b3ac11e5c9cd4aed8529b6c2cc3f3334 Package: iChip Version: 1.58.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: 43a3df92f00307f42bb0e122c351785c Package: iClusterPlus Version: 1.40.0 Depends: R (>= 4.1.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: ca2020d9a2e92843dca2191d926fd36b Package: iCNV Version: 1.24.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: 26d2140413df9425ec2240db9db13c9b Package: iCOBRA Version: 1.32.0 Depends: R (>= 4.4.0) Imports: shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2, ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR, markdown, utils, rlang Suggests: knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 6e56e7884c181a690b72a02638071833 Package: ideal Version: 1.28.0 Depends: topGO Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc, methods Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR License: MIT + file LICENSE MD5sum: c261e6ab39fdffce8f50469765669529 Package: IdeoViz Version: 1.40.0 Depends: R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer, graphics, GenomeInfoDb License: GPL-2 MD5sum: 254653b2d6e51b1febe613272b986a5d Package: idiogram Version: 1.80.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: f016295237d9f2899d743fb7c743a02b Package: idpr Version: 1.14.0 Depends: R (>= 4.1.0) Imports: ggplot2 (>= 3.3.0), magrittr (>= 1.5), dplyr (>= 0.8.5), plyr (>= 1.8.6), jsonlite (>= 1.6.1), rlang (>= 0.4.6), Biostrings (>= 2.56.0), methods (>= 4.0.0) Suggests: knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr License: LGPL (>= 3) MD5sum: ed93e289e1d948ab81c459ca7e68f22a Package: idr2d Version: 1.18.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>= 1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1), grDevices, grid, idr (>= 1.2), IRanges (>= 2.18.0), magrittr (>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats, stringr (>= 1.3.1), utils Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: cdcd7b2334807677f242889b2e6ef322 Package: IFAA Version: 1.6.0 Depends: R (>= 4.2.0), Imports: mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI (>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11), parallelly , glmnet, stats, utils, SummarizedExperiment, stringr, S4Vectors, DescTools, MatrixExtra, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: 0853c91afbd3c00f8ec2dd1d03fcf980 Package: iGC Version: 1.34.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 MD5sum: 74d03e9e471365be86f026751482b618 Package: IgGeneUsage Version: 1.18.0 Depends: R (>= 4.2.0) Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment, tidyr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork License: MIT + file LICENSE MD5sum: 9e3a9261f6d7432e0a24a73c9596c9d0 Package: igvR Version: 1.24.0 Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.17.1) Imports: methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo License: MIT + file LICENSE MD5sum: 22504cd9571c26da191af900b4122690 Package: igvShiny Version: 1.0.0 Depends: R (>= 3.5.0), GenomicRanges, methods, shiny Imports: BiocGenerics, checkmate, futile.logger, GenomeInfoDbData, htmlwidgets, httr, jsonlite, randomcoloR, RCurl, utils Suggests: BiocStyle, GenomicAlignments, knitr, Rsamtools, rtracklayer, RUnit, shinytest2, VariantAnnotation License: MIT + file LICENSE MD5sum: 50bbdf4bd61771f5f3bc8f53d67f577d Package: IHW Version: 1.32.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: e25b8024a43e84cbc88b432237468913 Package: illuminaio Version: 0.46.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: ce274cb32350919d0922b3ab593d6d94 Package: ILoReg Version: 1.14.0 Depends: R (>= 4.0.0) Imports: Matrix, parallel, foreach, aricode, LiblineaR, SparseM, ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster, parallelDist, cluster, dendextend, DescTools, plyr, scales, pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment, SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 2f86f0eba8a1eed60101d53081ce88e6 Package: IMAS Version: 1.28.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, IVAS Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats, ggfortify, grDevices, methods, Matrix, utils, graphics, gridExtra, grid, lattice, Rsamtools, survival, BiocParallel, GenomicAlignments, parallel Suggests: BiocStyle, RUnit License: GPL-2 MD5sum: ed30b053a9b5cfc8a038b455caab3bf4 Package: IMMAN Version: 1.24.0 Imports: STRINGdb, pwalign, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 2a49133cf0eb35887f11550db9b356ef Package: immunoClust Version: 1.36.0 Depends: R(>= 3.6), flowCore Imports: methods, stats, graphics, grid, lattice, grDevices Suggests: BiocStyle, utils, testthat License: Artistic-2.0 MD5sum: f6a8ac5555e46e8ef8c18c92917292ee Package: immunotation Version: 1.12.0 Depends: R (>= 4.1) Imports: stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr, xml2, maps, rlang Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT License: GPL-3 MD5sum: 126469e4b53ed5758f5ef1d53ab633de Package: IMPCdata Version: 1.40.0 Depends: R (>= 2.3.0) Imports: rjson License: file LICENSE MD5sum: ce40199fe36d68f7225d2b17b6b6c4a4 Package: impute Version: 1.78.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 0d422efa838131c97482584090a90260 Package: INDEED Version: 2.18.0 Depends: glasso (>= 1.8), R (>= 3.5) Imports: devtools (>= 1.13.0), graphics (>= 3.3.1), stats (>= 3.3.1), utils (>= 3.3.1), igraph (>= 1.2.4), visNetwork(>= 2.0.6) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) License: Artistic-2.0 MD5sum: bb9d450aabfe0001e90afadfdf8ddce9 Package: iNETgrate Version: 1.2.0 Depends: R (>= 4.3.0), BiocStyle (>= 2.18.1) Imports: SummarizedExperiment, GenomicRanges (>= 1.24.1), stats, WGCNA, grDevices, graphics, survival, igraph, Pigengene (>= 1.19.26), Homo.sapiens, glmnet, caret, gplots, minfi, matrixStats, Rfast, tidyr, tidyselect, utils Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks (>= 2.29.4) License: GPL-3 MD5sum: 75c31ea7e427e476d98213794f449e37 Package: infercnv Version: 1.20.0 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: b4800cedcc34306c658bc00df2489e0d Package: infinityFlow Version: 1.14.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 MD5sum: bc3f347fbf62b290dba5c39a64b73040 Package: Informeasure Version: 1.14.0 Depends: R (>= 4.0) Imports: entropy Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 892d83d482a067213d7146262374e759 Package: InPAS Version: 2.12.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq, depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges, GenomicFeatures, ggplot2, IRanges, limma, magrittr,methods,parallelly, plyranges, preprocessCore, readr,reshape2, RSQLite, stats,S4Vectors, utils Suggests: BiocGenerics,BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 2) MD5sum: e3d9b24e65d03afe5b16e28e40ef9d97 Package: INPower Version: 1.40.0 Depends: R (>= 3.1.0), mvtnorm Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 79f7a8d12c1b43d7d33b06cdd7bcaf91 Package: INSPEcT Version: 1.34.0 Depends: R (>= 3.6), methods, Biobase, BiocParallel Imports: pROC, deSolve, rootSolve, KernSmooth, readxl, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem, rtracklayer, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 8bfb6594cced6fbd9a4d9e9dd6d3bedd Package: INTACT Version: 1.4.0 Depends: R (>= 4.3.0) Imports: SQUAREM, bdsmatrix, numDeriv, stats, tidyr Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE MD5sum: 29f50fb862b2f11d762e9e4f2825ab05 Package: InTAD Version: 1.24.0 Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment,stats Imports: BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue, ggplot2,utils,ggpubr Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 71101e2ff7456beca3f359191f7fcc83 Package: intansv Version: 1.44.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: MIT + file LICENSE MD5sum: 1acee875b34a5813b47d7abda458108a Package: interacCircos Version: 1.14.0 Depends: R (>= 4.1) Imports: RColorBrewer, htmlwidgets, plyr, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: ddaeb5b2cb5e884f03e065beff3b6644 Package: InteractionSet Version: 1.32.0 Depends: GenomicRanges, SummarizedExperiment Imports: methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12), IRanges, GenomeInfoDb LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: aff48a3abadd50563c815f90e3ad6b79 Package: InteractiveComplexHeatmap Version: 1.12.0 Depends: R (>= 4.0.0), ComplexHeatmap (>= 2.11.0) Imports: grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>= 0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils, svglite, htmltools, clisymbols, jsonlite, RColorBrewer, fontawesome Suggests: knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges, data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap, cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3, GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks License: MIT + file LICENSE MD5sum: 29b464b431d25161d8c943ad076370ad Package: interactiveDisplay Version: 1.42.0 Depends: R (>= 3.5.0), methods, BiocGenerics, grid Imports: interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer, ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 MD5sum: 47260b1ea0a61bcba526cf19dbeedcdd Package: interactiveDisplayBase Version: 1.42.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 MD5sum: 1bfc6331eef1532bd20d7c92d7ecf98c Package: InterCellar Version: 2.10.0 Depends: R (>= 4.1) Imports: config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + file LICENSE MD5sum: 54dfbb6fcf648cfc35e22c302433faa1 Package: IntEREst Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles Imports: seqLogo, Biostrings, GenomicFeatures, txdbmaker, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: 7250fbe6412e72bb00fce1b740df39d4 Package: InterMineR Version: 1.26.0 Depends: R (>= 3.4.1) Imports: Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods Suggests: BiocStyle, Gviz, knitr, rmarkdown, GO.db, org.Hs.eg.db License: LGPL MD5sum: 0e5b41a9bbbb6d4ee29fc3c96eb2a1cf Package: IntramiRExploreR Version: 1.26.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: 0a8af24da7c639ce518ddc76023ae538 Package: IONiseR Version: 2.28.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 65cba501aaca631e83a431a5222b919d Package: iPAC Version: 1.48.0 Depends: R(>= 2.15), scatterplot3d, Biostrings, pwalign, multtest Imports: grDevices, graphics, stats, gdata License: GPL-2 MD5sum: 5ac2e6b60ae7de40623f6f457528717c Package: iPath Version: 1.10.0 Depends: R (>= 4.1), mclust, BiocParallel, survival Imports: Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer, stats LinkingTo: Rcpp, RcppArmadillo Suggests: rmarkdown, BiocStyle, knitr License: GPL-2 MD5sum: a6087d78da547464ea813f148556f5ad Package: ipdDb Version: 1.22.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 0df0fb01be9e82d47dfcc1beed10debf Package: IRanges Version: 2.38.1 Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.39.2), S4Vectors (>= 0.33.3) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 0850d03063f2fe4412dcede15862e595 Package: ISAnalytics Version: 1.14.0 Depends: R (>= 4.3) Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, DT Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture License: CC BY 4.0 MD5sum: c0cb43c05401cb60610ee9a3eb7fdd58 Package: iSEE Version: 2.16.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools License: MIT + file LICENSE MD5sum: 73072759d9857b0fa98b15822ef469ff Package: iSEEde Version: 1.2.0 Depends: iSEE Imports: DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3ec2ae8d7bf5c3693ebd2bba0fc82d00 Package: iSEEfier Version: 1.0.0 Imports: iSEE, iSEEu, methods, ggplot2, igraph, rlang, stats, SummarizedExperiment, SingleCellExperiment, visNetwork, BiocBaseUtils Suggests: knitr, rmarkdown, scater, scRNAseq, org.Mm.eg.db, scuttle, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 3fd2db87a8ffe65fed3bed2c8032309b Package: iSEEhex Version: 1.6.0 Depends: SummarizedExperiment, iSEE Imports: ggplot2, hexbin, methods, shiny Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater License: Artistic-2.0 MD5sum: bba278f2942fae967eadbeb08ad75d8b Package: iSEEhub Version: 1.6.0 Depends: SummarizedExperiment, SingleCellExperiment, ExperimentHub Imports: AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs, S4Vectors, shiny, shinydashboard, shinyjs, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData Enhances: BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 MD5sum: aafb27cf3482ad8563f2f1dd77179f5b Package: iSEEindex Version: 1.2.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: BiocFileCache, DT, iSEE, methods, paws.storage, rintrojs, shiny, shinydashboard, shinyjs, stringr, urltools, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), yaml License: Artistic-2.0 MD5sum: a77122c92de06e2d8bb2ba27c9c050a9 Package: iSEEpathways Version: 1.2.0 Depends: iSEE Imports: ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: dd7aff30ac39a4327af826e1b25c539e Package: iSEEu Version: 1.16.0 Depends: iSEE, iSEEhex Imports: methods, S4Vectors, IRanges, shiny, SummarizedExperiment, SingleCellExperiment, ggplot2 (>= 3.4.0), DT, stats, colourpicker, shinyAce Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr License: MIT + file LICENSE MD5sum: 3a78d7ef5f33d96e634b328e64b21098 Package: iSeq Version: 1.56.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 014bab8c2970fb5ee4a1e88bdf60ef00 Package: ISLET Version: 1.6.0 Depends: R(>= 4.2.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics, lme4, nnls Imports: stats, methods, purrr, abind Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr License: GPL-2 MD5sum: c726adb67a05474e557c4b312537889b Package: isobar Version: 1.50.0 Depends: R (>= 2.10.0), Biobase, stats, methods Imports: distr, plyr, biomaRt, ggplot2 Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 MD5sum: b4431dccee5efea35c238e489a29f441 Package: IsoBayes Version: 1.2.2 Depends: R (>= 4.3.0) Imports: methods, Rcpp, data.table, glue, stats, doParallel, parallel, doRNG, foreach, iterators, ggplot2,HDInterval, SummarizedExperiment, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 6f17f5aeddbdfc43d6b4dab3e2a3884c Package: IsoCorrectoR Version: 1.22.0 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 9ec780b864877f2a781e9b73dcfeb101 Package: IsoCorrectoRGUI Version: 1.20.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: a5f4e6224439488c6dd99ea8eeaf7a3a Package: IsoformSwitchAnalyzeR Version: 2.4.0 Depends: R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>= 3.3.5), pfamAnalyzeR Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment, tidyr, S4Vectors, BiocParallel, pwalign Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown License: GPL (>= 2) MD5sum: c5e04953cb25b3aa1e387b9efc6b935e Package: ISoLDE Version: 1.32.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) MD5sum: 7cbba9c4d35c8d91289c3adaf47eba2d Package: isomiRs Version: 1.32.1 Depends: R (>= 4.4), SummarizedExperiment Imports: AnnotationDbi, BiocGenerics, Biobase, broom, cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr, GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid, grDevices, graphics, GGally, limma, methods, RColorBrewer, readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble Suggests: knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 53ac57507cf4ca320a5e75b5a5103b9f Package: ITALICS Version: 2.64.0 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 MD5sum: b4915acf93933469c99658bf24605716 Package: iterativeBMA Version: 1.62.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 89a8b61f80ad7ca556e0dce5a6083449 Package: iterativeBMAsurv Version: 1.62.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) MD5sum: fc6561527ddf86dd86703e85ff69e394 Package: iterClust Version: 1.26.0 Depends: R (>= 3.4.1) Imports: Biobase, cluster, stats, methods Suggests: tsne, bcellViper License: file LICENSE MD5sum: eabf67932a07ea78a5a59325d9668045 Package: IVAS Version: 2.24.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, Biobase Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify, grDevices, methods, Matrix, BiocParallel,utils, stats Suggests: BiocStyle License: GPL-2 MD5sum: a9e16946c0fe23055ca470f6228979a1 Package: ivygapSE Version: 1.26.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: shiny, survival, survminer, hwriter, plotly, ggplot2, S4Vectors, graphics, stats, utils, UpSetR Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat, rmarkdown, BiocStyle, magick, statmod, codetools License: Artistic-2.0 MD5sum: 7fb095b6d3776b2c917f0e362e907a93 Package: IWTomics Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) MD5sum: b3828f438d53f59d79e0cb36470008f5 Package: karyoploteR Version: 1.30.0 Depends: R (>= 3.4), regioneR, GenomicRanges, methods Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset License: Artistic-2.0 MD5sum: 6382a475070cf7c3b14bc1f4c9084554 Package: katdetectr Version: 1.6.0 Depends: R (>= 4.2) Imports: Biobase (>= 2.54.0), BiocParallel (>= 1.26.2), BSgenome (>= 1.62.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.4), changepoint (>= 2.2.3), changepoint.np (>= 1.0.3), checkmate (>= 2.0.0), dplyr (>= 1.0.8), GenomeInfoDb (>= 1.28.4), GenomicRanges (>= 1.44.0), ggplot2 (>= 3.3.5), ggtext (>= 0.1.1), IRanges (>= 2.26.0), maftools (>= 2.10.5), methods (>= 4.1.3), plyranges (>= 1.17.0), Rdpack (>= 2.3.1), rlang (>= 1.0.2), S4Vectors (>= 0.30.2), scales (>= 1.2.0), tibble (>= 3.1.6), tidyr (>= 1.2.0), tools, utils, VariantAnnotation (>= 1.38.0) Suggests: BiocStyle (>= 2.26.0), knitr (>= 1.37), rmarkdown (>= 2.13), stats, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 2ca57fa26cee0e7fcd79a8ce1e1cc17f Package: KBoost Version: 1.12.0 Depends: R (>= 4.1), stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 | GPL-3 MD5sum: bab2b19bee27ed475cbe5c79e7c6f35b Package: KCsmart Version: 2.62.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 MD5sum: b3ed5b7e50556ca6a3d5baf4b906702c Package: kebabs Version: 1.38.0 Depends: R (>= 3.3.0), Biostrings (>= 2.35.5), kernlab Imports: methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector (>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: 98381dcc4ebca2f147b47e447b9eb8f4 Package: KEGGgraph Version: 1.64.0 Depends: R (>= 3.5.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: d5e889fc1ef57c5321c8780d6fb477c7 Package: KEGGlincs Version: 1.30.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 74c582aaea54a45d23f81c2691248c81 Package: keggorthology Version: 2.56.0 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 MD5sum: 691497adba5f91d8545854166be9a39b Package: KEGGREST Version: 1.44.1 Depends: R (>= 3.5.0) Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, knitr, markdown License: Artistic-2.0 MD5sum: 2bb51d65f60bb739a5d12a8849aaeebd Package: KinSwingR Version: 1.22.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 76d50e6a17fee8a4734a63181f1fadb1 Package: kissDE Version: 1.24.0 Imports: aods3, Biobase, DESeq2, DSS, ggplot2, gplots, graphics, grDevices, matrixStats, stats, utils, foreach, doParallel, parallel, shiny, shinycssloaders, ade4, factoextra, DT Suggests: BiocStyle, testthat License: GPL (>= 2) MD5sum: 0ca729fdae7a50b6d87c1986eb4fd7d5 Package: KnowSeq Version: 1.18.0 Depends: R (>= 4.0), cqn (>= 1.28.1) Imports: stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab, rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML, praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3), limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra Suggests: knitr License: GPL (>= 2) MD5sum: cd51bff29969954e1714f3bc382545d7 Package: knowYourCG Version: 1.0.0 Depends: R (>= 4.4.0) Imports: sesameData, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils Suggests: testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr, sesame, gprofiler2 License: MIT + file LICENSE MD5sum: 8c7dc7967fd1c15ab5559a8e39afb414 Package: LACE Version: 2.8.0 Depends: R (>= 4.2.0) Imports: curl, igraph, foreach, doParallel, sortable, dplyr, forcats, data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils, purrr, stringi, stringr, Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs, data.table, htmltools, htmlwidgets, bsplus, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr, ggplot2, svglite Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown License: file LICENSE MD5sum: 1f06d44181c05498e17014a064341fea Package: lapmix Version: 1.70.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) MD5sum: a9064f75e4664529fc520835dbf072dd Package: LBE Version: 1.72.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue License: GPL-2 MD5sum: 2ecc7ae0406b31187131cfba7a3964fb Package: ldblock Version: 1.34.0 Depends: R (>= 3.5), methods, rlang Imports: BiocGenerics (>= 0.25.1), httr, Matrix Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) License: Artistic-2.0 MD5sum: 50998c6eb25c8c3f27407aaded17d4b6 Package: LEA Version: 3.16.0 Depends: R (>= 3.3.0), methods, stats, utils, graphics Suggests: knitr License: GPL-3 MD5sum: ebc0cbbf4a27e629cd813fcc3cf170cd Package: LedPred Version: 1.38.0 Depends: R (>= 3.2.0), e1071 (>= 1.6) Imports: akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE MD5sum: 5ac06ad28b1f4b0a3a9357255bdfc414 Package: lefser Version: 1.14.0 Depends: SummarizedExperiment, R (>= 4.0.0) Imports: coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, testthat, pkgdown, covr, withr License: Artistic-2.0 MD5sum: 7c0450a5b6a2454d365ebfcfe8a4f68f Package: lemur Version: 1.2.0 Depends: R (>= 4.1) Imports: stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang, vctrs, glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, harmony (>= 1.0.3), limma, BiocNeighbors LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 9e609a4c3a6d2fdf1424d4a395958a38 Package: les Version: 1.54.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: cc926265521b2760680670870133c6f9 Package: levi Version: 1.22.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods, rmarkdown LinkingTo: Rcpp Suggests: rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 28efad2f3241af8f353ae24be5591891 Package: lfa Version: 2.4.0 Depends: R (>= 4.0) Imports: utils, methods, corpcor, RSpectra Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: 90494467097f449948bc69106b75428a Package: limma Version: 3.60.3 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods, statmod Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn License: GPL (>= 2) MD5sum: 5c96a6bd682a97b5faab490542f85edb Package: limmaGUI Version: 1.80.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: 81e7193849e140ea121d1709c704d358 Package: limpca Version: 1.0.0 Depends: R (>= 3.5.0) Imports: ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 374ba15f26d23379469833ad784163c0 Package: lineagespot Version: 1.8.0 Imports: VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9fb98621ae45e36c609c4fdfdcab6b9f Package: LinkHD Version: 1.18.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: d8fd011ebe2d95576e81284875d91840 Package: Linnorm Version: 2.28.0 Depends: R(>= 4.1.0) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats License: MIT + file LICENSE MD5sum: 1b64a21932d0c416c26852b6e7beccc2 Package: LinTInd Version: 1.8.0 Depends: R (>= 4.0), ggplot2, parallel, stats, S4Vectors Imports: data.tree, reshape2, networkD3, stringdist, purrr, ape, cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap, Biostrings, pwalign, IRanges, BiocGenerics(>= 0.36.1), ggtree Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: f8919ccf61d0e0ae90774318bfcc5aed Package: lionessR Version: 1.18.0 Depends: R (>= 3.6.0) Imports: stats, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE MD5sum: c2084ef989a7098d9ffc3596848e08c3 Package: lipidr Version: 2.18.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat License: MIT + file LICENSE MD5sum: 88ab1f2b6715c48ed6adf8db063a9a22 Package: LiquidAssociation Version: 1.58.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: f6351218c18b04888b9aa7900153bed9 Package: lisaClust Version: 1.12.1 Depends: R (>= 4.0) Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap, spatstat.random Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 4078683f9781e58a14dc5165fc63f7ae Package: lmdme Version: 1.46.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) MD5sum: 7b3cc0dccd73826ccc016f57f887c065 Package: loci2path Version: 1.24.0 Depends: R (>= 3.5.0) Imports: pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1412f642091b2926f1e994f649b643d5 Package: logicFS Version: 2.24.0 Depends: LogicReg, mcbiopi, survival Imports: graphics, methods, stats Suggests: genefilter, siggenes License: LGPL (>= 2) MD5sum: b1e50ea40211893152f592bc86b8e615 Package: LOLA Version: 1.34.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown Enhances: simpleCache, qvalue, ggplot2 License: GPL-3 MD5sum: 71834db35f3ebc68da43144f992c79db Package: LoomExperiment Version: 1.22.0 Depends: R (>= 3.5.0), S4Vectors, SingleCellExperiment, SummarizedExperiment, methods, rhdf5, BiocIO Imports: DelayedArray, GenomicRanges, HDF5Array, Matrix, stats, stringr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate License: Artistic-2.0 MD5sum: 38272fa104a88174813835efb981b109 Package: LPE Version: 1.78.0 Depends: R (>= 2.10) Imports: stats License: LGPL MD5sum: be3ec1a2f0da46207095b63168f8c136 Package: lpNet Version: 2.36.0 Depends: lpSolve, KEGGgraph License: Artistic License 2.0 MD5sum: 6c6f07ff3b0e327e4d820c20af8bba77 Package: lpsymphony Version: 1.32.0 Depends: R (>= 3.0.0) Suggests: BiocStyle, knitr, testthat Enhances: slam License: EPL MD5sum: e5ea5be3366f069124b5961b35554b03 Package: LRBaseDbi Version: 2.14.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase Suggests: testthat, BiocStyle, AnnotationHub License: Artistic-2.0 MD5sum: 90b47b0acdc021aab430c1f4fb13f808 Package: LRcell Version: 1.12.0 Depends: R (>= 4.1), ExperimentHub, AnnotationHub Imports: BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: 1361ad314795098775d911658bd9d5aa Package: lumi Version: 2.56.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: 6eaac686a98082cec64982bdb07e1040 Package: lute Version: 1.0.0 Depends: R (>= 4.3.0), stats, methods, utils, SummarizedExperiment, SingleCellExperiment, BiocGenerics Imports: S4Vectors, Biobase, scran, dplyr, ggplot2 Suggests: nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub, DelayedMatrixStats, BisqueRNA, DelayedArray License: Artistic-2.0 MD5sum: b23b8c9967877f1794106a3698a9c64d Package: LymphoSeq Version: 1.32.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: 6f7ce7612d9db44f4264f93548f4cf1f Package: M3C Version: 1.26.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: 0bf2edfa3ad5ec0ab2ea5715d3e2c3e2 Package: M3Drop Version: 1.30.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase License: GPL (>= 2) MD5sum: 55051b09f917c401ae20d0179bed57f8 Package: m6Aboost Version: 1.10.0 Depends: S4Vectors, adabag, GenomicRanges, R (>= 4.1) Imports: dplyr, rtracklayer, BSgenome, Biostrings, utils, methods, IRanges, ExperimentHub Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: c3f9e881c55e423b85278fd080fd6714 Package: Maaslin2 Version: 1.18.0 Depends: R (>= 3.6) Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4, tibble Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: 906974571be2e858590e1795e8812254 Package: Macarron Version: 1.8.1 Depends: R (>= 4.2.0), SummarizedExperiment Imports: BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, httr, RJSONIO, logging, methods, utils Suggests: knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: e63ab7fd5eaa701530a2afa143bbefcc Package: maCorrPlot Version: 1.74.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) MD5sum: 3c400c8da787b6e2d47a86bd284e50da Package: MACSQuantifyR Version: 1.18.0 Imports: readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel, methods, stats, latticeExtra, lattice, rmarkdown, png, grid, gridExtra, prettydoc, rvest, xml2 Suggests: knitr, testthat, R.utils, spelling License: Artistic-2.0 MD5sum: 308505d3750bca16541b25027c5a279d Package: MACSr Version: 1.12.0 Depends: R (>= 4.1.0) Imports: utils, reticulate, S4Vectors, methods, basilisk, ExperimentHub, AnnotationHub Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata License: BSD_3_clause + file LICENSE MD5sum: 141e2d00807310710e06175376390625 Package: made4 Version: 1.78.0 Depends: RColorBrewer,gplots,scatterplot3d, Biobase, SummarizedExperiment Imports: ade4 Suggests: affy, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 4a52cb67496be9a77fc8bea88147e5b3 Package: MADSEQ Version: 1.30.0 Depends: R (>= 3.5.0), rjags (>= 4.6) Imports: VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors, methods, preprocessCore, GenomicAlignments, Rsamtools, Biostrings, GenomicRanges, IRanges, VariantAnnotation, SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics, stats, grDevices, utils, zlibbioc, vcfR Suggests: knitr License: GPL (>= 2) MD5sum: a1dbf402ae4615a440fa0e74db087297 Package: maftools Version: 2.20.0 Depends: R (>= 3.3) Imports: data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy LinkingTo: Rhtslib, zlibbioc Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, pheatmap, curl License: MIT + file LICENSE MD5sum: bde10806df9ae35b1db41409a59f04e5 Package: MAGAR Version: 1.12.0 Depends: R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm Imports: doParallel, igraph, bigstatsr, rjson, plyr, data.table, UpSetR, reshape2, jsonlite, methods, ff, argparse, impute, RnBeads.hg19, RnBeads.hg38, utils, stats Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager License: GPL-3 MD5sum: 1fb64f2f6b53165df5eef2b7baef0761 Package: MAGeCKFlute Version: 2.8.0 Depends: R (>= 4.1) Imports: Biobase, gridExtra, ggplot2, ggrepel, grDevices, grid, reshape2, stats, utils, DOSE, clusterProfiler, pathview, enrichplot, msigdbr, depmap Suggests: biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap, png, scales, sva, BiocManager License: GPL (>= 3) MD5sum: 05d778353534020af126519e5c901a07 Package: magpie Version: 1.4.0 Depends: R (>= 4.3.0) Imports: utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx, RColorBrewer, reshape2, TRESS Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle License: MIT + file LICENSE MD5sum: 866d55c1dc4169f9a31aebe0926fc84e Package: magrene Version: 1.6.0 Depends: R (>= 4.2.0) Imports: utils, stats, BiocParallel Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: f125e7bb6e4427069b9a197fbe3f6286 Package: MAI Version: 1.10.0 Depends: R (>= 3.5.0) Imports: caret, parallel, doParallel, foreach, e1071, future.apply, future, missForest, pcaMethods, tidyverse, stats, utils, methods, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 84bf900ce154920e4046f68b3f996148 Package: maigesPack Version: 1.68.0 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) MD5sum: 9a01070722fadbc937adc1f68ca0455d Package: makecdfenv Version: 1.80.0 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) MD5sum: 35da2188e880ecbed491c48a58e2a234 Package: MANOR Version: 1.76.0 Depends: R (>= 2.10) Imports: GLAD, graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, bookdown License: GPL-2 MD5sum: 5019a448fd03a44defa1f4913c602680 Package: MantelCorr Version: 1.74.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) MD5sum: 92e7c48bf76c4b05e604f2e0f3d626c9 Package: MAPFX Version: 1.0.0 Depends: R (>= 4.4.0) Imports: flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2, RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils, e1071, xgboost, parallel, pbapply, reshape2, gtools, utils, stats, cowplot, methods, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 2239622dc542d9517fdbf4a16027b88d Package: maPredictDSC Version: 1.42.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 MD5sum: f3a28d08134d51b6475ea60b8c375067 Package: mapscape Version: 1.28.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 8ab227f45b91a6b1128f5a427c6f2df9 Package: mariner Version: 1.4.0 Depends: R (>= 4.2.0) Imports: methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, plyranges, magrittr, dbscan, purrr, progress, GenomeInfoDb, strawr (>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel, IRanges, SummarizedExperiment, rhdf5, plotgardener, RColorBrewer, colourvalues, utils, grDevices, graphics, grid Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData License: GPL-3 MD5sum: 877ca49033a52c6f585cf98801b015f3 Package: marr Version: 1.14.0 Depends: R (>= 4.0) Imports: Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, covr License: GPL (>= 3) MD5sum: c6904dc0ea9afca1769dbddda0abb681 Package: marray Version: 1.82.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL MD5sum: 5e60091b33aa39bf412773dd12925de9 Package: martini Version: 1.24.0 Depends: R (>= 4.0) Imports: igraph (>= 1.0.1), Matrix, memoise (>= 2.0.0), methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats (>= 1.20.0), stats, utils, LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0) Suggests: biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>= 2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>= 0.12.2), knitr, testthat, readr, rmarkdown License: GPL-3 MD5sum: d6e428865d6c2f93fd1a7e4ead695eeb Package: maser Version: 1.22.0 Depends: R (>= 3.5.0), ggplot2, GenomicRanges Imports: dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats, utils, IRanges, methods, BiocGenerics, parallel, data.table Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub License: MIT + file LICENSE MD5sum: bbec06573435c0f3dbc0756ba6b0e227 Package: maSigPro Version: 1.76.0 Depends: R (>= 2.3.1) Imports: Biobase, graphics, grDevices, venn, mclust, stats, MASS License: GPL (>= 2) MD5sum: feab6b0e2172fa00bc9f66f695939da6 Package: maskBAD Version: 1.48.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) MD5sum: 325467decf902b653896f4f4ecdef0cd Package: MassArray Version: 1.56.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: a7b5e97748ecb05841c9934aa02f3cd0 Package: massiR Version: 1.40.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: c3e53cde2160786fd4065729403e1892 Package: MassSpecWavelet Version: 1.70.0 Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench License: LGPL (>= 2) MD5sum: 715d8decea83a4066835cbd65ff0d7be Package: mastR Version: 1.4.0 Depends: R (>= 4.3.0) Imports: AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr, graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb, org.Hs.eg.db, patchwork, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment, tidyr, utils Suggests: BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR License: MIT + file LICENSE MD5sum: ecd0411976fbc0b4397fdd3709b416de Package: matchBox Version: 1.46.0 Depends: R (>= 2.8.0) License: Artistic-2.0 MD5sum: 73e00a2186d2871c016bdfd59a95c0b5 Package: MatrixGenerics Version: 1.16.0 Depends: matrixStats (>= 1.0.0) Imports: methods Suggests: Matrix, sparseMatrixStats, SparseArray, DelayedArray, DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: 2f682fec9adf6f7ddd61bbb24f389c7b Package: MatrixQCvis Version: 1.12.0 Depends: SummarizedExperiment (>= 1.20.0), plotly (>= 4.9.3), shiny (>= 1.6.0) Imports: ComplexHeatmap (>= 2.7.9), dplyr (>= 1.0.5), ExperimentHub (>= 2.6.0), ggplot2 (>= 3.3.3), grDevices (>= 4.1.0), Hmisc (>= 4.5-0), htmlwidgets (>= 1.5.3), impute (>= 1.65.0), imputeLCMD (>= 2.0), limma (>= 3.47.12), MASS (>= 7.3-58.1), methods (>= 4.1.0), pcaMethods (>= 1.83.0), proDA (>= 1.5.0), rlang (>= 0.4.10), rmarkdown (>= 2.7), Rtsne (>= 0.15), shinydashboard (>= 0.7.1), shinyhelper (>= 0.3.2), shinyjs (>= 2.0.0), stats (>= 4.1.0), tibble (>= 3.1.1), tidyr (>= 1.1.3), umap (>= 0.2.7.0), UpSetR (>= 1.4.0), vsn (>= 3.59.1) Suggests: BiocGenerics (>= 0.37.4), BiocStyle (>= 2.19.2), hexbin (>= 1.28.2), httr (>= 1.4.7), jpeg (>= 0.1-10), knitr (>= 1.33), statmod (>= 1.5.0), testthat (>= 3.0.2) License: GPL-3 MD5sum: 96680e162ebed9421036174fb0ada059 Package: matter Version: 2.6.2 Depends: R (>= 4.0), BiocParallel, Matrix, methods Imports: BiocGenerics, ProtGenerics, digest, irlba, biglm, stats, stats4, graphics, grDevices, utils Suggests: BiocStyle, knitr, testthat, plotly License: Artistic-2.0 MD5sum: 0b19b93e42bf69b305c1b44f58c0669a Package: MBAmethyl Version: 1.38.0 Depends: R (>= 2.15) License: Artistic-2.0 MD5sum: 0a1a68d42650f45c0824f639b27a5c04 Package: MBASED Version: 1.38.0 Depends: RUnit, BiocGenerics, BiocParallel, GenomicRanges, SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: cb58d747084b8beb7fc6ebfb66997858 Package: MBCB Version: 1.58.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) MD5sum: 50bf20c30fb6d46ac4a0d7d921066acb Package: MBECS Version: 1.8.0 Depends: R (>= 4.1) Imports: methods, magrittr, phyloseq, limma, lme4, lmerTest, pheatmap, rmarkdown, cluster, dplyr, ggplot2, gridExtra, ruv, sva, tibble, tidyr, vegan, stats, utils, Matrix Suggests: knitr, markdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: ff058b87508ce84bec16cebc6144558d Package: mbkmeans Version: 1.20.0 Depends: R (>= 3.6) Imports: methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix, BiocParallel LinkingTo: Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: 3d5a28e354827bd03cf2f9bc1d805e95 Package: mBPCR Version: 1.58.0 Depends: oligoClasses, GWASTools Imports: Biobase, graphics, methods, utils, grDevices Suggests: xtable License: GPL (>= 2) MD5sum: b1b54373b20525c45476c74b664e10e0 Package: MBQN Version: 2.16.0 Depends: R (>= 3.6) Imports: stats, graphics, utils, limma (>= 3.30.13), SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0), BiocFileCache, rappdirs, xml2, RCurl, ggplot2, PairedData, rmarkdown Suggests: knitr License: GPL-3 + file LICENSE MD5sum: 8d4b9cc16d208c0ba8b82c3053ae39df Package: mbQTL Version: 1.4.0 Depends: R (>= 4.3.0) Imports: MatrixEQTL, dplyr, ggplot2, readxl, stringr, tidyr, metagenomeSeq, pheatmap, broom, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: a70d8e80cec7b3761363de406f52e61a Package: MBttest Version: 1.32.0 Depends: R (>= 3.3.0), stats, gplots, gtools,graphics,base, utils,grDevices Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 96d612090a24d0588627a2ee84b98a40 Package: MCbiclust Version: 1.28.0 Depends: R (>= 3.4) Imports: BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db, org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA License: GPL-2 MD5sum: 3dfd762252589d5552eb12b5ec3d3e9a Package: mCSEA Version: 1.24.0 Depends: R (>= 3.5), mCSEAdata, Homo.sapiens Imports: biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, methods, parallel, S4Vectors, stats, SummarizedExperiment, utils Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit License: GPL-2 MD5sum: 5d82f33ee2410f060d5d3b543a330ca1 Package: mdp Version: 1.24.0 Depends: R (>= 4.0) Imports: ggplot2, gridExtra, grid, stats, utils Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager License: GPL-3 MD5sum: 1e86e695466ec5293f487e839d68565f Package: mdqc Version: 1.66.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) MD5sum: fc7bba85aa86b32f640ed85a6a40634d Package: MDTS Version: 1.24.0 Depends: R (>= 3.5.0) Imports: GenomicAlignments, GenomicRanges, IRanges, Biostrings, DNAcopy, Rsamtools, parallel, stringr Suggests: testthat, knitr License: Artistic-2.0 MD5sum: e6bfed149f369582ab558c180c843085 Package: MEAL Version: 1.34.0 Depends: R (>= 3.6.0), Biobase, MultiDataSet Imports: GenomicRanges, limma, vegan, BiocGenerics, minfi, IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute, Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA, graphics, stats, utils, matrixStats Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata License: Artistic-2.0 MD5sum: 080ec41c0b7ba7b76b724cf2e4b751ee Package: MeasurementError.cor Version: 1.76.0 License: LGPL MD5sum: 385f0ababe35989a96d48b64890f7101 Package: MEAT Version: 1.16.0 Depends: R (>= 4.0) Imports: impute (>= 1.58), dynamicTreeCut (>= 1.63), glmnet (>= 2.0), grDevices, graphics, stats, utils, stringr, tibble, RPMM (>= 1.25), minfi (>= 1.30), dplyr, SummarizedExperiment, wateRmelon Suggests: knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: f40b3fa11d098cb9136af1ed68b43165 Package: MEB Version: 1.18.0 Depends: R (>= 3.6.0) Imports: e1071, edgeR, scater, stats, wrswoR, SummarizedExperiment, SingleCellExperiment Suggests: knitr,rmarkdown,BiocStyle License: GPL-2 MD5sum: f0d7a65f3838ff5d8da1029b81c15d48 Package: MEDIPS Version: 1.56.0 Depends: R (>= 3.0), BSgenome, Rsamtools Imports: GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle License: GPL (>= 2) MD5sum: 06fa487d7e2853e1e49797f0b99097cf Package: MEDME Version: 1.64.0 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) MD5sum: 2c9d492d1828aac9dbe0b75e23957b1c Package: megadepth Version: 1.14.0 Imports: xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat License: Artistic-2.0 MD5sum: 628350f3482eff3c413eb9caeeb03ed7 Package: MEIGOR Version: 1.38.0 Depends: R (>= 4.0), Rsolnp, snowfall, deSolve, CNORode Suggests: CellNOptR, knitr, BiocStyle License: GPL-3 MD5sum: 3ee880dbaddfa5c54c37ef199986ec5b Package: Melissa Version: 1.20.0 Depends: R (>= 3.5.0), BPRMeth, GenomicRanges Imports: data.table, parallel, ROCR, matrixcalc, mclust, ggplot2, doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm, truncnorm, assertthat, BiocStyle, stats, utils Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 00b86832d2bf1997927bc7c85813a3d3 Package: memes Version: 1.12.0 Depends: R (>= 4.1) Imports: Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2, ggseqlogo, magrittr, matrixStats, methods, patchwork, processx, purrr, rlang, readr, stats, tools, tibble, tidyr, utils, usethis, universalmotif (>= 1.9.3), xml2 Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE MD5sum: 6abf47af7c8eff58f4597e6a9d619175 Package: Mergeomics Version: 1.32.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 63d9216f2a1887a14e9386326875625f Package: MeSHDbi Version: 1.40.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 MD5sum: 8e67d2d262dd1a257983615488b49667 Package: meshes Version: 1.30.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, DOSE, enrichplot, GOSemSim, methods, utils, AnnotationHub, MeSHDbi, yulab.utils Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: caea5d6eca99a44e6da93f7069adf6a0 Package: meshr Version: 2.10.0 Depends: R (>= 4.1.0) Imports: markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils, fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite License: Artistic-2.0 MD5sum: cd48a68f692299bc3f345f4fd27a1a22 Package: MesKit Version: 1.14.0 Depends: R (>= 4.0.0) Imports: methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape (>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges, circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3), ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 453b2aaca799656b3244d28813d5e2fb Package: messina Version: 1.40.0 Depends: R (>= 3.1.0), survival (>= 2.37-4), methods Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) MD5sum: 34107dedf71efb70706e1a691f2cb936 Package: metabCombiner Version: 1.14.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: e352af40d342e37f088d52547dbbc071 Package: metabinR Version: 1.6.0 Depends: R (>= 4.3) Imports: methods, rJava Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: efccc34a159b4233621693890496ce02 Package: MetaboAnnotation Version: 1.8.1 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.13.2), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR Enhances: RMariaDB, RSQLite License: Artistic-2.0 MD5sum: d2ee2dca75d1971ff478d0dc34229a39 Package: MetaboCoreUtils Version: 1.12.0 Depends: R (>= 4.0) Imports: utils, MsCoreUtils, BiocParallel, methods, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, robustbase License: Artistic-2.0 MD5sum: 5c8020458b1edbb490e53d7a6a08d927 Package: metabolomicsWorkbenchR Version: 1.14.2 Depends: R (>= 4.0) Imports: data.table, httr, jsonlite, methods, MultiAssayExperiment, struct, SummarizedExperiment, utils Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png License: GPL-3 MD5sum: 3d05d8ed6b5142d29516688701c95f93 Package: metabomxtr Version: 1.38.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: 0ab063062f74c7655edc1e038356e1ce Package: MetaboSignal Version: 1.34.0 Depends: R(>= 3.3) Imports: KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: b82087650964b3b931d3a4d36304f460 Package: metaCCA Version: 1.32.0 Suggests: knitr License: MIT + file LICENSE MD5sum: b602d2fbf656ff2a7681bd5791c5c161 Package: MetaCyto Version: 1.26.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) MD5sum: 93589be0d1f6e32739c13511c392d027 Package: metagene2 Version: 1.20.0 Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2 Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: bf60856b53ef88d0d7376fa09375cbb0 Package: metagenomeSeq Version: 1.46.0 Depends: R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports: parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 41ee6a7d7cbcefde6f518f4160e174cb Package: metahdep Version: 1.62.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: 0eaab5ea377a54adea50892a547b6ae5 Package: MetaNeighbor Version: 1.24.0 Depends: R(>= 3.5) Imports: grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR License: MIT + file LICENSE MD5sum: 6ed73a37ceab98459304310781ecec66 Package: MetaPhOR Version: 1.6.0 Depends: R (>= 4.2.0) Imports: utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3 Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: Artistic-2.0 MD5sum: b913640e4cf6259c8f53f10a2e71f746 Package: metapod Version: 1.12.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 0ef8722d68065f3fcb97958aeaf8105f Package: metapone Version: 1.10.0 Depends: R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: methods Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: 65689feea6b32375b0a40e9f05ba1802 Package: metaSeq Version: 1.44.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: 6e59fb1aed004a0ece836e691737331f Package: metaseqR2 Version: 1.16.0 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, txdbmaker, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 97568504674a5fe51d42532fac3420d8 Package: MetaVolcanoR Version: 1.18.0 Depends: R (>= 4.1.1) Imports: methods, data.table, dplyr, tidyr, plotly, ggplot2, cowplot, parallel, metafor, metap, rlang, topconfects, grDevices, graphics, stats, htmlwidgets Suggests: knitr, markdown, rmarkdown, testthat License: GPL-3 MD5sum: c7e866ce5e00332f115b6d63224ca146 Package: MetCirc Version: 1.34.0 Depends: R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), Spectra (>= 1.4.3) Imports: ggplot2 (>= 3.2.1), MsCoreUtils (>= 1.9.2), S4Vectors (>= 0.22.0) Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), testthat (>= 2.2.1) License: GPL (>= 3) MD5sum: b7432677a5f915535c558460d293d8e6 Package: methimpute Version: 1.26.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 20b4049f708d7599497c4dd928afa36f Package: methInheritSim Version: 1.26.0 Depends: R (>= 3.5.0) Imports: methylKit, GenomicRanges, GenomeInfoDb, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 MD5sum: 3f8d4d39b3ba67b66d67af89c97d709f Package: methodical Version: 1.0.0 Depends: GenomicRanges, ggplot2, R (>= 4.2.0), SummarizedExperiment Imports: BiocParallel, Biostrings, BSgenome, cowplot, data.table, DelayedArray, dplyr, ExperimentHub, foreach, GenomeInfoDb, HDF5Array, IRanges, R.utils, RcppRoll, rhdf5, rtracklayer, S4Vectors, scales, tibble, tidyr Suggests: AnnotationHub, annotatr, BiocStyle, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, DESeq2, knitr, methrix, rmarkdown, TumourMethData License: GPL (>= 3) MD5sum: bfa311ac4dc50c6519a49e5a37d54172 Package: MethPed Version: 1.32.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: a93fc4211fed3c53f143d0321800c569 Package: methrix Version: 1.18.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 157a933e3888ae27640a89e9fdbd1785 Package: MethTargetedNGS Version: 1.36.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: e172f984565593a55cdc5a609d4f2d06 Package: MethylAid Version: 1.38.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: f05e154707db84713a13409ed507759d Package: methylCC Version: 1.18.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: 33a4b70c813acb4d7aaadb9de2ac589f Package: methylclock Version: 1.10.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: 09e399250b7c3e541f6ae35aa8064c6a Package: methylGSA Version: 1.22.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: 1eef50037df7900e815fe97153b6e953 Package: methyLImp2 Version: 1.0.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 85b458073c4a9291cb7bae638b2f2a07 Package: methylInheritance Version: 1.28.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim License: Artistic-2.0 MD5sum: a542c143553d7621e56ead3600e48927 Package: methylKit Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: defffbe1d2af1dcf8ed93caa8e881387 Package: MethylMix Version: 2.34.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 07e6226f1a36dbb5258c4ba912ad40d0 Package: methylMnM Version: 1.42.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 466d0a4aa8a56da5a2330216a9bf61cd Package: methylPipe Version: 1.38.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: 6eb7c81c16c160209afaea397174abb5 Package: methylscaper Version: 1.12.0 Depends: R (>= 4.1.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 MD5sum: 9b06c9635e71e8f4378b7191dd59c754 Package: MethylSeekR Version: 1.44.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) MD5sum: 7cea8ef60e2c91bcb7c72f2055d61203 Package: methylSig Version: 1.16.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: 22056e8ae6a5f353d5456706c39c7a85 Package: methylumi Version: 2.50.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: ecc80bc2f57a44e5c64a2aa3c9a06b67 Package: MetID Version: 1.22.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: 68906691fa144664061f365211575f5f Package: MetNet Version: 1.22.0 Depends: R (>= 4.0), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 3.5), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 3.6), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) MD5sum: 65ed1e0e64a6b24d8d2ae74914be89e1 Package: mfa Version: 1.26.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: d9e0af1bfc9121c4a659edc30ca2e705 Package: Mfuzz Version: 2.64.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 3a386b0c8e348dbce6e7b5d414fd805f Package: MGFM Version: 1.38.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: 0a8999accfde46cc148c3ba614dd4d4e Package: MGFR Version: 1.30.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: bcb2574878a60c17976a21cc2d0f1948 Package: MGnifyR Version: 1.0.0 Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment, SummarizedExperiment, BiocGenerics Imports: mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors, urltools, utils, tidyjson Suggests: biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick License: Artistic-2.0 | file LICENSE MD5sum: 33b3a658e0d31cf40459d5875e225dd7 Package: mgsa Version: 1.52.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 6c8c1346c5f8402a9133b4c775fbfc8c Package: mia Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment (>= 1.99.3), MultiAssayExperiment Imports: methods, stats, utils, MASS, ape, decontam, vegan, BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER, BiocParallel, DelayedArray, DelayedMatrixStats, scuttle, scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr, bluster, MatrixGenerics Suggests: testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: e88ceee3a58a2cc700143a8d92475856 Package: miaSim Version: 1.10.0 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: f93db2bbea3579254ee3fa45cf576b43 Package: miaViz Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia (>= 0.99), ggplot2, ggraph (>= 2.0) Imports: methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial, ggrepel, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets, bluster License: Artistic-2.0 | file LICENSE MD5sum: 8021ec72a8f08cc1b2433baa96b55edb Package: MiChip Version: 1.58.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 14d2a937b7ebc52d6722ba58f2a0b184 Package: microbiomeDASim Version: 1.18.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: c1c8e1407ba831b4d8a683991e332fb1 Package: microbiomeExplorer Version: 1.14.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 962cb5152128e312d00d9de4ad50f21e Package: microbiomeMarker Version: 1.10.0 Depends: R (>= 4.1.0) Imports: dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2, tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges, tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR, BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase, ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest, plotROC, vegan, pROC, BiocParallel Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr License: GPL-3 MD5sum: c655a73c109471c9498a966fe137dbf8 Package: MicrobiomeProfiler Version: 1.10.0 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: 44134abbc7908952b66c6b3200a56a43 Package: MicrobiotaProcess Version: 1.16.0 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager License: GPL (>= 3.0) MD5sum: 72a353205ea8f646e2666d388695441b Package: microRNA Version: 1.62.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: d77a1ddd599e6c71e18a3636f74ae1e9 Package: microSTASIS Version: 1.4.0 Depends: R (>= 4.2.0) Imports: BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr, TreeSummarizedExperiment Suggests: BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: GPL-3 MD5sum: b8d8e3f3ee276147491659326d41faa7 Package: MICSQTL Version: 1.2.2 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 MD5sum: d6fea46bffd291c636f0514efaea8c47 Package: miloR Version: 2.0.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods, igraph, irlba, utils, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, numDeriv LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics License: GPL-3 + file LICENSE MD5sum: 97710e35fb00571af5fa666d438d33ab Package: mimager Version: 1.28.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: 3f999178f84ec6d071afa82127b1ae17 Package: mina Version: 1.12.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL MD5sum: a3f67bad4120ab0e91dc8f9917f2c100 Package: MineICA Version: 1.44.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: d156b98e0cfe80b6f45faaab16d6a556 Package: minet Version: 3.62.0 Imports: infotheo License: Artistic-2.0 MD5sum: d41c2ee7886cd4054ebbc43d3d089b56 Package: minfi Version: 1.50.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: fd6c21fc94109f3df4868d467d728573 Package: MinimumDistance Version: 1.48.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 64da1e1bff8bf3c445b27f64aeaa7c5b Package: MiPP Version: 1.76.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: e8b3c6721f95cb4f0747d131192cf443 Package: miQC Version: 1.12.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 96a8c2a8056319d64abab9ded4c0cea0 Package: MIRA Version: 1.26.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 7ca75011403665f90e3dc4868586510e Package: MiRaGE Version: 1.46.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 28244077f0f388f30e1f61559c821d51 Package: miRBaseConverter Version: 1.28.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 8c3193852c955b0dcbab12b900b97e47 Package: miRcomp Version: 1.34.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: b5b105ee3069402c395bf82d9e7455c9 Package: mirIntegrator Version: 1.34.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: b8127b92b6bffcd70dd8e5d014ad3511 Package: MIRit Version: 1.0.0 Depends: MultiAssayExperiment, R (>= 4.4.0) Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, readxl, Rgraphviz (>= 2.44.0), rlang, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 03d54fcb9b259e85d7fc024905660e9a Package: miRLAB Version: 1.34.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: 80ca10e459b8f93e96f52c7ff0c0c6bc Package: miRmine Version: 1.26.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) MD5sum: a9487816b61260b9cc719681c351bd9e Package: miRNAmeConverter Version: 1.32.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: df0fa455daebebf661620ed66f9ff3d9 Package: miRNApath Version: 1.64.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: e2523c519d68fe6020e503c3b8589449 Package: miRNAtap Version: 1.38.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: f35eb840811a454ec8071c6d54e19096 Package: miRSM Version: 2.0.0 Depends: R (>= 3.5.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 7440af4ee4f90df400ae95ae3f404fb1 Package: miRspongeR Version: 2.8.0 Depends: R (>= 3.5.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: c91b8fc08b7a4fbd79c42907a179af32 Package: mirTarRnaSeq Version: 1.12.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils, viridis Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE MD5sum: 6660161ebf828ac9d01b071d03a35317 Package: missMethyl Version: 1.38.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: 420a5a1f7e76af1630b6c61bb5b62380 Package: missRows Version: 1.24.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: ae5b7f29eb5fd010de9a747e7b5c5677 Package: mitch Version: 1.16.0 Depends: R (>= 4.3) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE MD5sum: 8cc3c66176f69cb5500fd05ba737c9a9 Package: mitoClone2 Version: 1.10.0 Depends: R (>= 4.1.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: d8ed5dddc67c715a78ebd6281f599b29 Package: mixOmics Version: 6.28.0 Depends: R (>= 3.5.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl License: GPL (>= 2) MD5sum: a1a734c56d3532b2761d4d8f28b4caff Package: MLInterfaces Version: 1.84.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat Enhances: parallel License: LGPL MD5sum: d8d5c4defb73e6c8592dcc3883e8ba90 Package: MLSeq Version: 2.22.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 253baca09ff57ecede1dc3dcdfd0fc55 Package: MMDiff2 Version: 1.32.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 09bcd86391b568c98a08d6594a2f378f Package: MMUPHin Version: 1.18.1 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: 774949f2f0e384093741dae43d1e902c Package: mnem Version: 1.20.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: b5c450dcfb024f09010213bd41c35cfe Package: moanin Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: eef994ca1c5dd969f81d74412c90e929 Package: mobileRNA Version: 1.0.11 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, GenomeInfoDb, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 5d44c5617c834cb84d67b427e1dc6834 Package: MODA Version: 1.30.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 35e69a966a0aa47e54690e757f0b2fb5 Package: ModCon Version: 1.12.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: 9701ff6b028c438e6d625cea859d4147 Package: Modstrings Version: 1.20.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: e51f2b43fa20b16aff072241bd4fad56 Package: MOFA2 Version: 1.14.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE MD5sum: f26973bb886e42965da2285dcafdc93b Package: MOGAMUN Version: 1.14.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 63572c5ed46e5452b99350df73339527 Package: mogsa Version: 1.38.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: 89cc195bc0bc408179bb0aeef11510ae Package: MoleculeExperiment Version: 1.4.1 Depends: R (>= 2.10) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 390e166b982767bbf003b63d6ff37ba4 Package: MOMA Version: 1.16.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 1a07db91d88a9e852cd4fd2697496f22 Package: monocle Version: 2.32.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: 445fdc36d65ef51d5ae2e685e25a303d Package: Moonlight2R Version: 1.2.0 Depends: R (>= 4.3), doParallel, foreach Imports: parmigene, randomForest, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics, GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap, GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf, readr, seqminer, stringr, tibble, tidyHeatmap, tidyr, AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics, ggplot2, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 MD5sum: f475250cf6f2d5a55f1eb26625249224 Package: MoonlightR Version: 1.30.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) MD5sum: 517f9414cbedce5809f753e35fe11945 Package: mosaics Version: 2.42.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 88b6f315a30cdbe5b0f2633415e7a8b2 Package: mosbi Version: 1.10.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 4ded6176affbaf518aaa528c4e6d6ff5 Package: mosdef Version: 1.0.0 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE MD5sum: dfa580c3570313701fca2e668505b8ab Package: MOSim Version: 2.0.0 Depends: R (>= 4.2.0) Imports: HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2, lazyeval, matrixStats, methods, rlang, stringi, stringr, scran, Seurat, Signac, edgeR, Rcpp LinkingTo: cpp11, Rcpp Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster License: GPL-3 MD5sum: b72dccdba59e93f4542b6ca8cb7e34c5 Package: Motif2Site Version: 1.8.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: 32726330698a5598a6cc3b94768890eb Package: motifbreakR Version: 2.18.0 Depends: R (>= 4.3.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment, pwalign Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 MD5sum: 65c2d5ba2d583d50d7d9c2346c282f52 Package: motifcounter Version: 1.28.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: 8b7b7fabd40a8cfb328d5d37d9e97696 Package: MotifDb Version: 1.46.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: 2a97fdce4a3bd28c064d1cc9dcbbfcac Package: motifTestR Version: 1.0.3 Depends: Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0), Imports: GenomeInfoDb, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2bd31f634c36c0e6e64da03047f32056 Package: MouseFM Version: 1.14.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 1c3836f416a1d61053bfdf62757e9282 Package: MPFE Version: 1.40.0 License: GPL (>= 3) MD5sum: 9818852de1c7931c400acb2bcb7910aa Package: mpra Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 0ed549385244e900241cee7b171e61af Package: MPRAnalyze Version: 1.22.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 MD5sum: 2b8a6626fb3a7712693ac52e91f6e09b Package: msa Version: 1.36.0 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign License: GPL (>= 2) MD5sum: 203ad6442682aa7b422efa4eca58fe01 Package: MSA2dist Version: 1.8.0 Depends: R (>= 4.4.0) Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, pwalign, rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: 24edac924f4afc0a1b057631a42126d0 Package: MsBackendMassbank Version: 1.12.0 Depends: R (>= 4.0), Spectra (>= 1.9.12) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>= 1.35.3), MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown License: Artistic-2.0 MD5sum: 70e6f473926d981ed44ea5c74de7a4f1 Package: MsBackendMgf Version: 1.12.0 Depends: R (>= 4.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: d76a10d5ec189c072b1265e053a1dbf2 Package: MsBackendMsp Version: 1.8.0 Depends: R (>= 4.1.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: aad0088ec517645d4df723a7354c97a5 Package: MsBackendRawFileReader Version: 1.10.0 Depends: R (>= 4.1), methods, Spectra (>= 1.5.8) Imports: ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.10.1), utils, BiocParallel Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: 30d8d6d4170ede1226dd61db09859170 Package: MsBackendSql Version: 1.4.0 Depends: R (>= 4.2.0), Spectra (>= 1.9.12) Imports: BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3), DBI, MsCoreUtils, IRanges, data.table, progress, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR License: Artistic-2.0 MD5sum: 9f8ed0198c159e2a2300d94a345d9d53 Package: MsCoreUtils Version: 1.16.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats, clue LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest Enhances: HDF5Array License: Artistic-2.0 MD5sum: 1ce48d68f53ea2e2c938174d3267038c Package: MsDataHub Version: 1.4.0 Imports: ExperimentHub, utils Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3) License: Artistic-2.0 MD5sum: eb9738e107d9853464974f33cf9540b7 Package: MsExperiment Version: 1.6.0 Depends: R (>= 4.2), ProtGenerics (>= 1.35.2), Imports: methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures, DBI, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite License: Artistic-2.0 MD5sum: dd7b20fcaa327c677927b7325f72e993 Package: MsFeatures Version: 1.12.0 Depends: R (>= 4.1) Imports: methods, ProtGenerics (>= 1.23.5), MsCoreUtils, SummarizedExperiment, stats Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 0cf76757173ea60e8788184044eeb190 Package: msgbsR Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: 4c60770e6958e896f47d53729c406c5b Package: msImpute Version: 1.14.0 Depends: R (>= 3.5.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD License: GPL (>= 2) MD5sum: ad1b2c83f60061a30d8c7118619400b9 Package: msmsEDA Version: 1.42.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: aeb5a74ee3094fec64080134277900a6 Package: msmsTests Version: 1.42.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue Suggests: xtable License: GPL-2 MD5sum: 865a6c3cb6e0ad6a68b3485b5d0f24e6 Package: MSnbase Version: 2.30.1 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), mzR (>= 2.29.3), S4Vectors, ProtGenerics (>= 1.29.1) Imports: MsCoreUtils, PSMatch, BiocParallel, IRanges (>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment License: Artistic-2.0 MD5sum: bb892e2db1c7edd63d5c2f140c76ea24 Package: msPurity Version: 1.30.1 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: f4a6e1d9c62e000bb7186e42365aa3e9 Package: msqrob2 Version: 1.12.0 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr License: Artistic-2.0 MD5sum: e01c31da8335ff50cf16782b2e182bd1 Package: MsQuality Version: 1.4.0 Depends: R (>= 4.2.0) Imports: BiocParallel (>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), msdata (>= 0.32.0), MsExperiment (>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics (>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.5.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra (>= 1.13.2), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), utils (>= 4.2.0) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) License: GPL-3 MD5sum: 6cf41d34dc678322b5020647f651f20c Package: MSstats Version: 4.12.0 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, checkmate, MASS, htmltools, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, plotly, marray, stats, grDevices, graphics, methods, statmod, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown License: Artistic-2.0 MD5sum: db3384b73e5c932a33c098d65539d238 Package: MSstatsBig Version: 1.2.0 Imports: arrow, DBI, dplyr, MSstats, MSstatsConvert, readr, sparklyr, utils Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 97b7eb5cb3ee1dc84adb512eda1816b4 Package: MSstatsConvert Version: 1.14.0 Depends: R (>= 4.0) Imports: data.table, log4r, methods, checkmate, utils, stringi Suggests: tinytest, covr, knitr, rmarkdown License: Artistic-2.0 MD5sum: 6a21f469e875bcf8e06ce6def76fb441 Package: MSstatsLiP Version: 1.10.0 Depends: R (>= 4.1) Imports: dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight License: Artistic-2.0 MD5sum: cd5cdff62e2d200032d08462df619bac Package: MSstatsLOBD Version: 1.12.0 Depends: R (>= 4.0) Imports: minpack.lm, ggplot2, utils, stats, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr License: Artistic-2.0 MD5sum: e16f8bdc282367180a96ca15025545cc Package: MSstatsPTM Version: 2.6.0 Depends: R (>= 4.3) Imports: dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel LinkingTo: Rcpp Suggests: knitr, rmarkdown, tinytest, covr License: Artistic-2.0 MD5sum: a230b4b93be950b89c9b6434d8f9195c Package: MSstatsQC Version: 2.22.0 Depends: R (>= 3.5.0) Imports: dplyr,plotly,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: 24ab7c72850b9c9b6f28274fa50d42b7 Package: MSstatsQCgui Version: 1.24.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 MD5sum: 65ad5b406d000626e3347274ad9e7447 Package: MSstatsShiny Version: 1.6.2 Depends: R (>= 4.2) Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2,plotly, data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics,mockery Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2, License: Artistic-2.0 MD5sum: b3e59f6e507940f0f2fa466dbcc67a26 Package: MSstatsTMT Version: 2.12.1 Depends: R (>= 4.2) Imports: limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate, plotly, htmltools Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: eb65603f8250470311f0e9a400bc553a Package: MuData Version: 1.8.0 Depends: Matrix, S4Vectors, rhdf5 Imports: methods, stats, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, DelayedArray Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater License: GPL-3 MD5sum: 2dc2604e1899ce3779ebd229627de89b Package: Mulcom Version: 1.54.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: 25fe3a720b35c315e1c8b4ef9fe266e3 Package: MultiAssayExperiment Version: 1.30.2 Depends: SummarizedExperiment (>= 1.3.81), R (>= 3.5.0) Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, methods, S4Vectors, tidyr, utils Suggests: BiocStyle, HDF5Array, knitr, maftools, R.rsp, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR License: Artistic-2.0 MD5sum: 1d152835882cf196bd0b311b57165851 Package: MultiBaC Version: 1.14.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix, grDevices, pcaMethods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: d8c9c895cd6bc613a5f6d6149be3ef03 Package: multiClust Version: 1.34.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 650264c35e5626985cc2a92fa6611878 Package: multicrispr Version: 1.14.0 Depends: R (>= 4.0) Imports: BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: 579fcee16a1d43bc83bd1de1f79f79c4 Package: MultiDataSet Version: 1.32.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 9c914dbe2c300a925e438d114b09a09a Package: multiGSEA Version: 1.14.0 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: 94c441a11b1d8cc26100bb6a72d9f51d Package: multiHiCcompare Version: 1.22.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 4d22c6584a4568785d9fed5a2a60da09 Package: MultiMed Version: 2.26.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: d3344a711cca5cd4f5c4f211b923de03 Package: multiMiR Version: 1.26.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: bd852665039e26601b48a88c6fee941c Package: MultimodalExperiment Version: 1.4.0 Depends: R (>= 4.3.0), IRanges, S4Vectors Imports: BiocGenerics, MultiAssayExperiment, methods, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 40bda593146ce76bfa895e79c920038b Package: multiOmicsViz Version: 1.28.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL MD5sum: 0be559c1344279157e4cb6d8132a7c2e Package: MultiRNAflow Version: 1.2.0 Depends: Mfuzz (>= 2.58.0), R (>= 4.3) Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.14.0), DESeq2 (>= 1.38.1), factoextra (>= 1.0.7), FactoMineR (>= 2.6), ggalluvial (>= 0.12.3), ggplot2 (>= 3.4.0), ggplotify (>= 0.1.2), ggrepel (>= 0.9.2), gprofiler2 (>= 0.2.1), graphics (>= 4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>= 1.4), plot3Drgl (>= 1.0.3), reshape2 (>= 1.4.4), S4Vectors (>= 0.36.2), stats (>= 4.2.2), SummarizedExperiment (>= 1.28.0), UpSetR (>= 1.4.0), utils (>= 4.2.2) Suggests: BiocGenerics (>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 | file LICENSE MD5sum: 01d7daf3e1f4d4e309fe30865da82d0f Package: multiscan Version: 1.64.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: 337ad7dac22d9879042b5b270b1e14ca Package: multiWGCNA Version: 1.2.0 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 MD5sum: 2638d256d44750a93d32f8941ea6ad2b Package: multtest Version: 2.60.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: dc068497c9617c5e9e573135c7e94e4a Package: mumosa Version: 1.12.0 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: c8e9a9849b00fb60e850f1b053bf1b96 Package: MungeSumstats Version: 1.12.0 Depends: R(>= 4.1) Imports: magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, stringr, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer(>= 1.59.1), RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 MD5sum: a822d5f2fcb92b031910ad6e761ef3d0 Package: muscle Version: 3.46.0 Depends: Biostrings License: Unlimited MD5sum: a6cac8eaf2ba6101084d34cbb9429d8f Package: musicatk Version: 1.14.0 Depends: R (>= 4.0.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, deconstructSigs, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1) Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 MD5sum: db5dc9b568c34d30dbc3312134db99f6 Package: MVCClass Version: 1.78.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 3738d139a2790a4aef9df482c5a889fa Package: MWASTools Version: 1.28.0 Depends: R (>= 3.5.0) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: 80fea7863311aeb1e2d203a58a858b11 Package: mygene Version: 1.40.0 Depends: R (>= 3.2.1), GenomicFeatures, txdbmaker Imports: methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7), Hmisc, sqldf, plyr, S4Vectors Suggests: BiocStyle License: Artistic-2.0 MD5sum: b62ae0c707a5c6bda499de45d36f81f7 Package: myvariant Version: 1.34.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 2b9f8488e550c0c955e05f61096f9d0e Package: mzID Version: 1.42.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 81597dfd83c9bebab487872f39902746 Package: mzR Version: 2.38.0 Depends: R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown License: Artistic-2.0 MD5sum: b33fdb33c573e4ee70c482dcb9a0ee25 Package: NADfinder Version: 1.28.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown License: GPL (>= 2) MD5sum: ce66e1db757a63f63b267cab0dc005a2 Package: NanoMethViz Version: 3.0.2 Depends: R (>= 4.0.0), methods, ggplot2 (>= 3.4.0) Imports: cpp11 (>= 0.2.5), readr, cli, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, data.table, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), scico, stats, stringr, tibble, tidyr, utils, withr, zlibbioc LinkingTo: Rcpp Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: 0be73619502b16886e29c6d2766c0988 Package: NanoStringDiff Version: 1.34.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: 2a319368dcb3e2645ea6e61acd7e6c4b Package: NanoStringNCTools Version: 1.12.0 Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2 Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf License: MIT MD5sum: 68c0534038f2fc888d921a4a0445e800 Package: NanoTube Version: 1.10.0 Depends: R (>= 4.1), Biobase, ggplot2, limma Imports: fgsea, methods, reshape, stats, utils Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx License: GPL-3 + file LICENSE MD5sum: 225b8b792ddf2c051421b989d783a7ad Package: NBAMSeq Version: 1.20.0 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: a95388a516212cae0fa91faedd3c0c81 Package: ncdfFlow Version: 2.50.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), methods, BH Imports: Biobase,BiocGenerics,flowCore,zlibbioc LinkingTo: cpp11,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr MD5sum: 94add381e58322c6517ecdd98900ffaa Package: ncRNAtools Version: 1.14.0 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: e393c77669318a72dfac7d1adbfa1f9f Package: ndexr Version: 1.26.0 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: c80d25673fe8098835f90e1e6bfcb0a8 Package: nearBynding Version: 1.14.0 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: a3364fc178c11f562287736b372ef5ff Package: Nebulosa Version: 1.14.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods, ggrastr Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat License: GPL-3 MD5sum: aef561cce8f3fc1e548c424e49f9ecaa Package: NeighborNet Version: 1.22.0 Depends: methods Imports: graph, stats License: CC BY-NC-ND 4.0 MD5sum: 75be6973cd4d274d29b318dda111c91c Package: nempi Version: 1.12.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle License: GPL-3 MD5sum: 48ce3a40492c279e6b9bc0da8b8fdeae Package: NetActivity Version: 1.6.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE MD5sum: 20c438c1093e971d22c85d29ab3c7a56 Package: netboost Version: 2.12.0 Depends: R (>= 4.0.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, BiocStyle, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, rmarkdown License: GPL-3 OS_type: unix MD5sum: 80b62061467fb9f7cd614abb52b059d1 Package: nethet Version: 1.36.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: c6cf73fdf8dff2675628bcf5fd53c71c Package: netprioR Version: 1.30.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: e5bbdd4271f24bbe99c5854f8295a313 Package: netresponse Version: 1.64.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: 04c5386ccb9b694ce5ed85cc9c66508e Package: NetSAM Version: 1.44.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db (>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1) Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown License: LGPL MD5sum: ede9882b75032f49eb66be3387e8a7ac Package: netSmooth Version: 1.24.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: ad5ca980c022a5a3d89d68935b0fd085 Package: netZooR Version: 1.8.0 Depends: R (>= 4.2.0), igraph, reticulate, pandaR, yarn, matrixcalc Imports: RCy3, viridisLite, STRINGdb, Biobase, GOstats, AnnotationDbi, matrixStats, GO.db, org.Hs.eg.db, Matrix, gplots, nnet, data.table, vegan, stats, utils, reshape, reshape2, penalized, parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS, assertthat, tidyr, methods, dplyr, graphics Suggests: testthat (>= 2.1.0), knitr, rmarkdown, pkgdown License: GPL-3 MD5sum: 658bb8ca933920a19d6c1048fc567644 Package: NewWave Version: 1.14.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: 299026953ce2e2d0f84d30ae764dbcf2 Package: ngsReports Version: 2.6.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.5.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm License: LGPL-3 MD5sum: 73930d3448526ab4d460cd8df37457e0 Package: nipalsMCIA Version: 1.2.0 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 MD5sum: 01514ba68df9ed1585127886dc8dc32e Package: nnNorm Version: 2.68.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: d96f2c1ff5b559bb4046dc38997bb542 Package: nnSVG Version: 1.8.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: cfa3c76e456f2894aa9cf4bb217775d6 Package: NOISeq Version: 2.48.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 266ebb7663e3cac3d44bcc2eb0ebffc5 Package: NoRCE Version: 1.16.0 Depends: R (>= 4.2.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,GenomeInfoDb, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown License: MIT + file LICENSE MD5sum: e79da3417649bcffdc1369c68475af18 Package: normalize450K Version: 1.32.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: f06afe5dcc8d2f35938515026058aebc Package: NormalyzerDE Version: 1.22.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: 98c26a0455b43da1d9118a273d0dc43e Package: NormqPCR Version: 1.50.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: c1f9f2980c036c3d12da969a9e0cbf8d Package: normr Version: 1.30.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: 567b9ce69ad2f45088f774b569997baa Package: NPARC Version: 1.16.0 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: 2048fe6cd5f80784418237ac6e64c4eb Package: npGSEA Version: 1.40.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 940b70ed26fec0ee7072fd067f58dcc2 Package: NTW Version: 1.54.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: bb8eb153cc3ab2a5e8e67a3370d1ee06 Package: nucleoSim Version: 1.32.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 6b8bd4a8882b36984b1e2dfa0b44e464 Package: nucleR Version: 2.36.0 Depends: R (>= 3.5.0), methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: d45f809204c39579b453bb6bedeb14ac Package: nuCpos Version: 1.22.0 Depends: R (>= 4.2.0) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 MD5sum: fe89fc612f08f5029da61cd75d6a904a Package: nullranges Version: 1.10.0 Imports: stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment License: GPL-3 MD5sum: 16467b15b49c8b43068a9bd075f05cb3 Package: NuPoP Version: 2.12.0 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: d3497a2315e4b2666b9e14338f99b9a8 Package: occugene Version: 1.64.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: 5e1a7ed239fddce895f5fe631473d573 Package: OCplus Version: 1.78.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, interp License: LGPL MD5sum: 554ed296dbf1262ec3f36db177c3bee3 Package: octad Version: 1.6.0 Depends: R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2, limma, rhdf5, foreach, Rfast, octad.db, stats, httr, qpdf, ExperimentHub, AnnotationHub, Biobase, S4Vectors Imports: EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2, grDevices, utils Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 6a7fdf5c475a25e5fa5afb6efcfa988b Package: odseq Version: 1.32.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE MD5sum: b11bc43ede0c213716fe4eea30848135 Package: OGRE Version: 1.8.0 Depends: R (>= 4.2.0), S4Vectors Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS,tidyr Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) License: Artistic-2.0 MD5sum: ddaaa9c9e73292a70ac62161894baeb7 Package: oligo Version: 1.68.2 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: 67a4a81464fade64ad5b9938f9e467e2 Package: oligoClasses Version: 1.66.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 77101fb516ca594b625fa927c1ca6857 Package: OLIN Version: 1.82.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 95337b40ee103a1f3edac277c8d42c65 Package: OLINgui Version: 1.78.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: 33df9a074405ccd2fb7de4293389fa07 Package: omada Version: 1.6.0 Depends: pdfCluster (>= 1.0-3), kernlab (>= 0.9-29), R (>= 4.2), fpc (>= 2.2-9), Rcpp (>= 1.0.7), diceR (>= 0.6.0), ggplot2 (>= 3.3.5), reshape (>= 0.8.8), genieclust (>= 1.1.3), clValid (>= 0.7), glmnet (>= 4.1.3), dplyr(>= 1.0.7), stats (>= 4.1.2), clValid(>= 0.7) Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: eef21ed4466576a66db1a7863fb19fe6 Package: OmaDB Version: 2.20.0 Depends: R (>= 3.5), httr (>= 1.2.1), plyr(>= 1.8.4) Imports: utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: f5ebe6a825ded34027fae435bda860e2 Package: omicade4 Version: 1.44.0 Depends: R (>= 3.0.0), ade4 Imports: made4, Biobase Suggests: BiocStyle License: GPL-2 MD5sum: 0f3d29001db656000decc2393ea9e86f Package: OmicCircos Version: 1.42.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 MD5sum: 885df8d13657ede029636e48e641ca6c Package: omicplotR Version: 1.24.0 Depends: R (>= 3.6), ALDEx2 (>= 1.18.0) Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: d764c73a88e5c8c37861d7d4d0bd4bf7 Package: omicRexposome Version: 1.26.0 Depends: R (>= 3.5.0), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: bfb418bc08b4b20c99b3699535323ee7 Package: OMICsPCA Version: 1.22.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: f1355a08b4f6084e1456f7bbe974ccec Package: omicsPrint Version: 1.24.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: b6a45eba371b40d174fdb2ee1d4174bd Package: omicsViewer Version: 1.8.0 Depends: R (>= 4.2) Imports: survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders, ROCR, drc Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 MD5sum: eb4d1b484969c040a583635ae83fa638 Package: Omixer Version: 1.14.0 Depends: R (>= 4.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: e5ab349488a77b85389f2511448110ea Package: OmnipathR Version: 3.11.10 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), httr, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml Suggests: BiocStyle, biomaRt, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, sigmajs, smoof, supraHex, testthat License: MIT + file LICENSE MD5sum: f9a265a9a003f50b7ffbdcf13851d537 Package: ompBAM Version: 1.8.0 Imports: utils, Rcpp, zlibbioc Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 803e1300a839bd4e907b1283d9142a13 Package: oncomix Version: 1.26.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 845acc8f7e402773a7870f0dd09b2824 Package: oncoscanR Version: 1.6.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: dc6db50c110da450b480a855acbd07dd Package: OncoScore Version: 1.32.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 9b8c5ee284d93343d22c697f5d98fdc3 Package: oneSENSE Version: 1.26.0 Depends: R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d Imports: Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: 1b7432c64a38ffdf0bb16f5241f094bb Package: ontoProc Version: 1.26.0 Depends: R (>= 4.0), ontologyIndex Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi License: Artistic-2.0 MD5sum: 2be593b51266b0f77150987813198a96 Package: openCyto Version: 2.16.1 Depends: R (>= 3.5.0) Imports: methods,Biobase,BiocGenerics,flowCore(>= 1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>= 3.99.1),flowClust(>= 3.11.4),RBGL,graph,data.table,RColorBrewer LinkingTo: cpp11, BH Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS MD5sum: 989527c028a208399495262e31d7c5dd Package: openPrimeR Version: 1.26.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), pwalign, XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0) Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) License: GPL-2 MD5sum: 0cf5c83f6925fe0c0810687de06428c1 Package: openPrimeRui Version: 1.26.0 Depends: R (>= 4.0.0), openPrimeR (>= 0.99.0) Imports: shiny (>= 1.0.2), shinyjs (>= 0.9), shinyBS (>= 0.61), DT (>= 0.2), rmarkdown (>= 1.0) Suggests: knitr (>= 1.13) License: GPL-2 MD5sum: e06faf02809699e7e2298c31897f7ca0 Package: OpenStats Version: 1.16.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, utils Suggests: rmarkdown License: GPL (>= 2) MD5sum: 22c40ac9ac2814d7ffce8913715035f2 Package: oposSOM Version: 2.22.0 Depends: R (>= 4.0.0), igraph (>= 1.0.0) Imports: fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl LinkingTo: RcppParallel, Rcpp License: GPL (>= 2) MD5sum: 386c1fc5e32d54ca7df5b8c83e0f1970 Package: oppar Version: 1.32.0 Depends: R (>= 3.3) Imports: Biobase, methods, GSEABase, GSVA Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel License: GPL-2 MD5sum: 367fcda9c679358cdb035c7945573c51 Package: oppti Version: 1.18.0 Depends: R (>= 3.5) Imports: limma, stats, reshape, ggplot2, grDevices, RColorBrewer, pheatmap, knitr, methods, devtools, parallelDist, Suggests: markdown License: MIT MD5sum: e94920b2dd69ead57107d64f17f90968 Package: optimalFlow Version: 1.16.0 Depends: dplyr, optimalFlowData, rlang (>= 0.4.0) Imports: transport, parallel, Rfast, robustbase, dbscan, randomForest, foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 90c9915af15f1f669f58cbff2998318c Package: OPWeight Version: 1.26.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: 9f1457e1348768eb02aa1fc822b36c2c Package: OrderedList Version: 1.76.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 6b17307fd64aeaac78001738453d0edd Package: ORFhunteR Version: 1.12.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: MIT License MD5sum: 669c56e51b739eaf56e4085f685b78f1 Package: ORFik Version: 1.24.0 Depends: R (>= 4.4.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), curl, RCurl, data.table (>= 1.11.8), DESeq2 (>= 1.24.0), downloader, fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools, txdbmaker, utils, XML, xml2 (>= 1.2.0), withr LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: ab04051f8a3466ec859a0e3bb4091156 Package: OrganismDbi Version: 1.46.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.31.13), txdbmaker Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 27dcef7928fa7de607912c9be634af58 Package: Organism.dplyr Version: 1.32.0 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: 661562ae1c787acf9e783c9b20f75463 Package: orthogene Version: 1.10.0 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, grr, repmis, ggtree, tools Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB License: GPL-3 MD5sum: 2d974edb32db6fbad4e0335fb8747a38 Package: orthos Version: 1.2.0 Depends: R (>= 4.3), SummarizedExperiment Imports: AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2, ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras, methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ae6fb7c22acd9936cdeddf8c6c2e80b2 Package: OSAT Version: 1.52.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 13752ed186f1f704bb3a2a603b50e0a9 Package: Oscope Version: 1.34.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: 3432d44dc42c94cb4db2a13657bdf986 Package: OTUbase Version: 1.54.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: 1c1b710ef954e59c719ebd630f14e7d4 Package: OUTRIDER Version: 1.22.0 Depends: R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods Imports: BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics, GenomicRanges, ggplot2, ggrepel, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, reshape2, S4Vectors, scales, splines, stats, txdbmaker, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase License: MIT + file LICENSE MD5sum: ec5b68d0beea7c2d9ca980b2de00d797 Package: OutSplice Version: 1.4.0 Depends: R(>= 4.3) Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0), GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0) Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: ee4aa9e815520ec8770900f6a5a03743 Package: OVESEG Version: 1.20.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: 58626ff5ed07f419c553c3ee9ad69c65 Package: PAA Version: 1.38.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: e9170b6028877d47771085f4cdc09abd Package: packFinder Version: 1.16.0 Depends: R (>= 4.1.0) Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle License: GPL-2 MD5sum: 53559b1586134e302253d52f2e97f803 Package: padma Version: 1.14.1 Depends: R (>= 4.1.0), SummarizedExperiment, S4Vectors Imports: FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot, reshape2 License: GPL (>= 3) MD5sum: 08d2b2562be17089c10e2edca243d538 Package: PADOG Version: 1.46.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: doParallel, parallel License: GPL (>= 2) MD5sum: d187f648fb5ad0642bf2ed3c01ea9660 Package: PAIRADISE Version: 1.20.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: a19a6f836f92423db0b92507d7a3ea81 Package: paircompviz Version: 1.42.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) MD5sum: d1314b15414c3811c7c96ccfd31b8e5f Package: pairedGSEA Version: 1.4.0 Depends: R (>= 4.3.0) Imports: DESeq2, DEXSeq, limma, fgsea, sva, SummarizedExperiment, S4Vectors, BiocParallel, ggplot2, aggregation, stats, utils, methods Suggests: writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle License: MIT + file LICENSE MD5sum: 020392f3a389eee727c2802eecd4cadf Package: pairkat Version: 1.10.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, KEGGREST, igraph, data.table, methods, stats, magrittr, CompQuadForm, tibble Suggests: rmarkdown, knitr, BiocStyle, dplyr License: GPL-3 MD5sum: 73e864d2cbb04d075831160fb9d17ea2 Package: pandaR Version: 1.36.0 Depends: R (>= 3.0.0), methods, Biobase, BiocGenerics, Imports: matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit, hexbin Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 4e48842390c4c780e54f87abd6783302 Package: panelcn.mops Version: 1.26.0 Depends: R (>= 3.5.0), cn.mops, methods, utils, stats, graphics Imports: GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb, grDevices Suggests: knitr, rmarkdown, RUnit, BiocGenerics License: LGPL (>= 2.0) MD5sum: 9b9e51e256dc2f0c528df3b85c90f3e0 Package: PanomiR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, GSEABase, igraph, limma, metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer, rlang, tibble, withr, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: e08849113aba6605cf8b11f304871498 Package: panp Version: 1.74.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) MD5sum: 83950b6e5e2faae3cee277b0d868dc4f Package: PANR Version: 1.50.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils, RedeR Suggests: snow License: Artistic-2.0 MD5sum: d3124b49947a1c2a84a8ac0256e59031 Package: PanViz Version: 1.6.0 Depends: R (>= 4.2.0) Imports: tidyr, stringr, dplyr, tibble, magrittr, futile.logger, utils, easycsv, rentrez, igraph, RColorBrewer, data.table, colorspace, grDevices, rlang, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3, License: Artistic-2.0 MD5sum: a86a36e3d1d1d0257716e40eb6017c16 Package: pareg Version: 1.8.0 Depends: R (>= 4.2), tensorflow (>= 2.2.0), tfprobability (>= 0.10.0) Imports: stats, tidyr, purrr, future, doFuture, foreach, doRNG, tibble, glue, tidygraph, igraph, proxy, dplyr, magrittr, ggplot2, ggraph, rlang, progress, Matrix, keras, nloptr, ggrepel, methods, DOSE, stringr, reticulate, logger, hms, devtools, basilisk Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea, ComplexHeatmap, GGally, ggsignif, circlize, enrichplot, ggnewscale, tidyverse, cowplot, ggfittext, simplifyEnrichment, GSEABenchmarkeR, BiocParallel, ggupset, latex2exp, org.Hs.eg.db, GO.db License: GPL-3 MD5sum: e49dabbc53813030a5e2ab64f8d2b8ed Package: parglms Version: 1.36.0 Depends: methods Imports: BiocGenerics, BatchJobs, foreach, doParallel Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gwascat, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 744f580953968903c2f349ee6c6d0f12 Package: parody Version: 1.62.0 Depends: R (>= 3.5.0), tools, utils Suggests: knitr, BiocStyle, testthat, rmarkdown License: Artistic-2.0 MD5sum: c8196533b9ce0fe0c30b53fbc36ac875 Package: partCNV Version: 1.2.0 Depends: R (>= 3.5.0) Imports: stats, data.table, depmixS4, Seurat, SingleCellExperiment, AnnotationHub, magrittr, GenomicRanges Suggests: BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0) License: GPL-2 MD5sum: 4bd01c230a50c92595857ea5d73e8b82 Package: PAST Version: 1.20.0 Depends: R (>= 4.0) Imports: stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges, S4Vectors Suggests: knitr, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: 508ec5d38565e824f0621b3b1b869749 Package: Path2PPI Version: 1.34.0 Depends: R (>= 3.2.1), igraph (>= 1.0.1), methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: 7089dbe5dcf9abcf0489d73085cb26f5 Package: pathifier Version: 1.42.0 Imports: R.oo, princurve (>= 2.0.4) License: Artistic-1.0 MD5sum: a72b766643987b1eb0141d485b43ffd6 Package: pathlinkR Version: 1.0.1 Depends: R (>= 4.3.0) Imports: circlize, clusterProfiler, ComplexHeatmap, dplyr, ggforce, ggplot2, ggpubr, ggraph, ggrepel, grid, igraph, purrr, sigora, stringr, tibble, tidygraph, tidyr, vegan, visNetwork Suggests: AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite, knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0), vdiffr License: GPL-3 + file LICENSE MD5sum: 7647c4fd7f4c6c1bc61fb25f63eb4232 Package: PathNet Version: 1.44.0 Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 MD5sum: 97d15779057c023dee37bc2ed0793ec2 Package: PathoStat Version: 1.30.0 Depends: R (>= 3.5) Imports: limma, corpcor,matrixStats, reshape2, scales, ggplot2, rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats, methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2, ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 2648d3326944a7b2253febbdc2b55918 Package: pathRender Version: 1.72.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: edcd0637a90f269ddd1e136fe2747258 Package: pathVar Version: 1.34.0 Depends: R (>= 3.3.0), methods, ggplot2, gridExtra Imports: EMT, mclust, Matching, data.table, stats, grDevices, graphics, utils License: LGPL (>= 2.0) MD5sum: f32e5bae7380c4d8da80e8294b81b876 Package: pathview Version: 1.44.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, org.EcK12.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 9ae0cf4f69b470f26cf9c3adcd54db3d Package: pathwayPCA Version: 1.20.0 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 MD5sum: 5511e0148b9680bc5bc81e1ae1e5bbc1 Package: pcaExplorer Version: 2.30.0 Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools License: MIT + file LICENSE MD5sum: eb5d127db03c7354b421414876d41556 Package: pcaMethods Version: 1.96.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) MD5sum: 48e3e0060da13311fb64ce4b5a5a95b6 Package: PCAN Version: 1.32.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 MD5sum: cf0d63aa4ddbec2cbb8c5fd903b38570 Package: PCAtools Version: 2.16.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown License: GPL-3 MD5sum: 26cdc8bb4b8a97bad091121c8a447cc8 Package: pcxn Version: 2.26.0 Depends: R (>= 3.4), pcxnData Imports: methods, grDevices, utils, pheatmap Suggests: igraph, annotate, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 113121a843d42f6416007b0b480c97a6 Package: PDATK Version: 1.12.0 Depends: R (>= 4.1), SummarizedExperiment Imports: data.table, MultiAssayExperiment, ConsensusClusterPlus, igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro, CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE MD5sum: c867495fe32e84c022aaf79725384429 Package: pdInfoBuilder Version: 1.68.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 MD5sum: 724b3046d660166a4f57158d4599b2a4 Package: PeacoQC Version: 1.14.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2, grDevices, grid, gridExtra, methods, plyr, stats, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 3) MD5sum: 51b67554e2fc3c687b3d066f701af3e6 Package: PECA Version: 1.40.0 Depends: R (>= 3.3) Imports: ROTS, limma, affy, genefilter, preprocessCore, aroma.affymetrix, aroma.core Suggests: SpikeIn License: GPL (>= 2) MD5sum: df000dd7ee1d55e9782751867eeb3a7a Package: peco Version: 1.16.0 Depends: R (>= 3.5.0) Imports: assertthat, circular, conicfit, doParallel, foreach, genlasso (>= 1.4), graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: 94cdeab6764f56208e93ab36588ede10 Package: Pedixplorer Version: 1.0.0 Depends: R (>= 4.3.0) Imports: graphics, stats, methods, ggplot2, utils, grDevices, stringr, plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, testthat Suggests: diffviewer, vdiffr, rmarkdown, BiocStyle, knitr, withr, magick License: Artistic-2.0 MD5sum: 6746f8804d616b4ab81f9a5c5e88f8a3 Package: pengls Version: 1.10.0 Depends: R (>= 4.2.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: 21bc8e1c16147bc0892f23d7f5f7e12e Package: PepsNMR Version: 1.22.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE MD5sum: f1282c5663f5256222aeab08f9d10bbc Package: pepStat Version: 1.38.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 MD5sum: 1060461884e2aae9a706e8ca6e0101a8 Package: pepXMLTab Version: 1.38.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 47a209049f41351be54787a151f6288c Package: PERFect Version: 1.18.0 Depends: R (>= 3.6.0), sn (>= 1.5.2) Imports: ggplot2 (>= 3.0.0), phyloseq (>= 1.28.0), zoo (>= 1.8.3), psych (>= 1.8.4), stats (>= 3.6.0), Matrix (>= 1.2.14), fitdistrplus (>= 1.0.12), parallel (>= 3.6.0) Suggests: knitr, rmarkdown, kableExtra, ggpubr License: Artistic-2.0 MD5sum: 1d7ff3a7be9d8efd2ee67db80b1445c5 Package: periodicDNA Version: 1.14.0 Depends: R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel Imports: S4Vectors, rtracklayer, stats, GenomeInfoDb, magrittr, zoo, ggplot2, methods, parallel, cowplot Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 + file LICENSE MD5sum: c116ab80e50452441f06e870076520b1 Package: pfamAnalyzeR Version: 1.4.0 Depends: R (>= 4.3.0), readr, stringr, dplyr Imports: utils, tibble, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 159f961b5c1cf72a7808ccc9be908580 Package: pgca Version: 1.28.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 671eb39ba4672ef9091002269ae5bdfe Package: pgxRpi Version: 1.0.3 Depends: R (>= 4.2) Imports: utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, plyr, GenomicRanges, SummarizedExperiment, S4Vectors, parallelly Suggests: BiocStyle, rmarkdown, knitr, testthat License: Artistic-2.0 MD5sum: de3ea03a18c961c67bfd9831e9d69da9 Package: phantasus Version: 1.24.0 Depends: R (>= 4.3) Imports: ggplot2, protolite, Biobase, GEOquery, Rook, htmltools, httpuv, jsonlite, limma, edgeR, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, data.table, curl, config (>= 0.3.2), rhdf5client (>= 1.25.1), yaml, fs, phantasusLite, XML Suggests: testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db License: MIT + file LICENSE MD5sum: 6cf0dbb0e3d7caba180409d7844d2dfb Package: phantasusLite Version: 1.2.0 Depends: R (>= 4.2) Imports: data.table, rhdf5client(>= 1.25.1), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE MD5sum: 4579bccaa73b58bf7fbde98f8c75e2b4 Package: PharmacoGx Version: 3.8.0 Depends: R (>= 3.6), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: b95948bc254f7d632d08e2b513b5f6f1 Package: PhenoGeneRanker Version: 1.12.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: 596b806ce5897636cf990d9e164b6beb Package: phenomis Version: 1.6.0 Depends: SummarizedExperiment Imports: Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: e5584b99a9512a85a06d812037b3acd0 Package: phenopath Version: 1.28.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: 59eb0de382112a838e83107fae0c7885 Package: phenoTest Version: 1.52.0 Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: c328e5a65fb23f41850ba33426555fce Package: PhenStat Version: 2.40.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: 1a5091ce06e2b18ab6b7304ef67b4569 Package: philr Version: 1.30.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: 2e520ccc88af18bc9d5bc24e855bedc7 Package: PhIPData Version: 1.12.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: 5808d8cdf3ced14d08106b4bcc688174 Package: phosphonormalizer Version: 1.28.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 7f10028f988dd2863a1146816cc374a1 Package: PhosR Version: 1.14.0 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: b3f0a2ac55de5cc2eb1c111be440c688 Package: PhyloProfile Version: 1.18.0 Depends: R (>= 4.3.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, OmaDB, plyr, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 17f697e79b9f3b4b97630d5fe3a6b323 Package: piano Version: 2.20.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: b17442413ad451f1687042ec9aa90579 Package: pickgene Version: 1.76.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 24af45d6d6ef2e0a0cb072ff71c87289 Package: PICS Version: 2.48.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: f623ebbba55b65f683be702090970861 Package: Pigengene Version: 1.30.0 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.28.0) Imports: bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy License: GPL (>= 2) MD5sum: 3d5675d20b410ab1075b2c0f66b9b88e Package: PING Version: 2.48.0 Depends: R(>= 3.5.0) Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, IRanges, GenomicRanges, S4Vectors Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 MD5sum: 3e04958697353eb22d7ccdb6aef3feec Package: pipeComp Version: 1.14.0 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL MD5sum: a25e5a539ced5b2ab8248a35e7420ffb Package: pipeFrame Version: 1.20.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 69757b1d6cff5093c75de715acf129e2 Package: PIPETS Version: 1.0.1 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 31aa1a52776aa26f78a236506bc78ac9 Package: PIUMA Version: 1.0.0 Depends: R (>= 4.3), ggplot2 Imports: cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales, Hmisc, patchwork, grDevices, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 + file LICENSE MD5sum: cb1b14530fd79279647c34be3bf261b2 Package: planet Version: 1.12.0 Depends: R (>= 4.3) Imports: methods, tibble, magrittr, dplyr Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 MD5sum: 1f5e0ac4cf03cdd864d8e52314d7c50c Package: planttfhunter Version: 1.4.0 Depends: R (>= 4.2.0) Imports: Biostrings, SummarizedExperiment, utils, methods Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: e8b3295f5c0010dc5a432aadc5fa3ffa Package: plasmut Version: 1.2.0 Depends: R (>= 4.3.0) Imports: tibble, stats, dplyr Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3418b0e591598ff7d3ba101c41ae1e47 Package: plgem Version: 1.76.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 MD5sum: 442e9fbb078b63f7c7a2f1486236cee1 Package: plier Version: 1.74.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: 2d2d194a21f3018ca3e61b368563b4dc Package: PloGO2 Version: 1.16.0 Depends: R (>= 4.0), GO.db, GOstats Imports: lattice, httr, openxlsx, xtable License: GPL-2 MD5sum: bf3209bd42c6ea1ab191349b34525bd8 Package: plotgardener Version: 1.10.2 Depends: R (>= 4.1.0) Imports: curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rlang, stats, strawr, tools, utils, withr LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: MIT + file LICENSE MD5sum: 8ee72993a7c4d069942eb944aded1b0b Package: plotGrouper Version: 1.22.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: ee8abbf272babac802dacd626c03f894 Package: PLPE Version: 1.64.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: dafce9c74ef3de7149bfb715775e0a41 Package: PLSDAbatch Version: 1.0.0 Depends: R (>= 4.3.0) Imports: mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr, lmerTest, performance, grid, stats, pheatmap, vegan, Biobase, BiocStyle, TreeSummarizedExperiment Suggests: knitr, rmarkdown, testthat, badger License: GPL-3 MD5sum: e20f0f98a9333a2942583fce5219b1a9 Package: plyinteractions Version: 1.2.0 Depends: R (>= 4.3.0) Imports: InteractionSet, GenomeInfoDb, BiocGenerics, GenomicRanges, plyranges, IRanges, S4Vectors, rlang, dplyr, tibble, tidyselect, methods, utils Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), RefManageR License: Artistic-2.0 MD5sum: dfcf6d2fbc9b2ff3e1fa21c961c8ea42 Package: pmm Version: 1.36.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 MD5sum: 08d78d57da38c41b08745424ff9e2813 Package: PoDCall Version: 1.12.0 Depends: R (>= 4.4) Imports: ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 19317ef000927e845bef3ad2d9dc985c Package: podkat Version: 1.36.0 Depends: R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges Imports: Rcpp (>= 0.11.1), parallel, stats (>= 4.3.0), graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome (>= 1.32.0) LinkingTo: Rcpp, Rhtslib (>= 1.15.3) Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr License: GPL (>= 2) MD5sum: 8207ea951937ea8e567ab1dbd72ad098 Package: pogos Version: 1.24.0 Depends: R (>= 3.5.0), rjson (>= 0.2.15), httr (>= 1.3.1) Imports: methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics Suggests: knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b8fdee2855bcc8b9f331a589f444ba66 Package: polyester Version: 1.39.0 Depends: R (>= 3.0.0) Imports: Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma, zlibbioc Suggests: knitr, ballgown, markdown License: Artistic-2.0 MD5sum: 1504375346264bbfe126942a12bf189f Package: POMA Version: 1.14.0 Depends: R (>= 4.0) Imports: broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, FSA, ggplot2, ggrepel, glmnet, impute, janitor, limma, lme4, magrittr, MASS, mixOmics, randomForest, RankProd (>= 3.14), rlang, SummarizedExperiment, sva, tibble, tidyr, utils, uwot, vegan Suggests: BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) License: GPL-3 MD5sum: e4c078133877b25c181028fbe493bdb9 Package: powerTCR Version: 1.24.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, purrr, stats, truncdist, vegan, VGAM Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 245ee8b94fbbb3bc71eb99d1539d7e3f Package: POWSC Version: 1.12.0 Depends: R (>= 4.1), Biobase, SingleCellExperiment, MAST Imports: pheatmap, ggplot2, RColorBrewer, grDevices, SummarizedExperiment, limma Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: d56b7bfdd31766253ef4bf3ec3f54212 Package: ppcseq Version: 1.12.0 Depends: R (>= 4.1.0), rstan (>= 2.18.1) Imports: benchmarkme, dplyr, edgeR, foreach, ggplot2, graphics, lifecycle, magrittr, methods, parallel, purrr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rlang, rstantools (>= 2.1.1), stats, tibble, tidybayes, tidyr (>= 0.8.3.9000), utils LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, testthat, BiocStyle, rmarkdown License: GPL-3 MD5sum: 0e1f68850251f2aaa1dae50f4887996b Package: PPInfer Version: 1.30.0 Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData Imports: httr, grDevices, graphics, stats, utils License: Artistic-2.0 MD5sum: 21c76cdc82498a60c43d9ec2d683759a Package: pqsfinder Version: 2.20.0 Depends: R (>= 3.5.0), Biostrings Imports: Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods LinkingTo: Rcpp, BH (>= 1.78.0) Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi License: BSD_2_clause + file LICENSE MD5sum: 3fcb21939b544939c8949ea01c05008d Package: pram Version: 1.20.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0), GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: d63f30651073eb0019d6b894bf142d09 Package: prebs Version: 1.44.0 Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, GenomeInfoDb, S4Vectors Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 MD5sum: dea42a05e4fc834b85ed7a225c421581 Package: preciseTAD Version: 1.14.0 Depends: R (>= 4.1) Imports: S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics, e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW, foreach, pbapply, stats, parallel, gtools, rCGH Suggests: knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle License: MIT + file LICENSE MD5sum: 043b5f807e6b2dc8f4e6ed2c15b85ac8 Package: PREDA Version: 1.50.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 MD5sum: f0bae192e0acdc90954f6c45f75d9251 Package: preprocessCore Version: 1.66.0 Imports: stats License: LGPL (>= 2) MD5sum: 9f1f733188487fcc35b228fccbcf1efa Package: PrInCE Version: 1.20.0 Depends: R (>= 3.6.0) Imports: purrr (>= 0.2.4), dplyr (>= 0.7.4), tidyr (>= 0.8.99), forecast (>= 8.2), progress (>= 1.1.2), Hmisc (>= 4.0), naivebayes (>= 0.9.1), robustbase (>= 0.92-7), ranger (>= 0.8.0), LiblineaR (>= 2.10-8), speedglm (>= 0.3-2), tester (>= 0.1.7), magrittr (>= 1.5), Biobase (>= 2.40.0), MSnbase (>= 2.8.3), stats, utils, methods, Rdpack (>= 0.7) Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 8f8209f9d84546d8761bb8fd548b86d3 Package: proActiv Version: 1.14.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2, IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments, GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang, scales, S4Vectors, SummarizedExperiment, stats, tibble, txdbmaker Suggests: testthat, rmarkdown, knitr, Rtsne, gridExtra License: MIT + file LICENSE MD5sum: a108dd1289b5185804cdb6ce6948aaf1 Package: proBAMr Version: 1.38.0 Depends: R (>= 3.0.1), IRanges, AnnotationDbi Imports: GenomicRanges, Biostrings, GenomicFeatures, txdbmaker, rtracklayer Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: c1f46f146bbd79c70aadcfb8e9da7336 Package: PROcess Version: 1.80.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 MD5sum: bd41f56e86912dcce4137e267b166f92 Package: procoil Version: 2.32.0 Depends: R (>= 3.3.0), kebabs Imports: methods, stats, graphics, S4Vectors, Biostrings, utils Suggests: knitr License: GPL (>= 2) MD5sum: de2eb89dd0b624ea94e17fb94c130e0e Package: proDA Version: 1.18.0 Imports: stats, utils, methods, BiocGenerics, SummarizedExperiment, S4Vectors, extraDistr Suggests: testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 54959ba1f95d57a70847ed6c8c7f5766 Package: profileplyr Version: 1.20.0 Depends: R (>= 3.6), BiocGenerics, SummarizedExperiment Imports: GenomicRanges, stats, soGGi, methods, utils, S4Vectors, R.utils, dplyr, magrittr, tidyr, IRanges, rjson, ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT, pheatmap, ggplot2, EnrichedHeatmap, ComplexHeatmap, grid, circlize, BiocParallel, rtracklayer, GenomeInfoDb, grDevices, rlang, tiff, Rsamtools Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Cairo License: GPL (>= 3) MD5sum: 9e7a04715fe576c324b1364820271391 Package: profileScoreDist Version: 1.32.0 Depends: R(>= 3.3) Imports: Rcpp, BiocGenerics, methods, graphics LinkingTo: Rcpp Suggests: BiocStyle, knitr, MotifDb License: MIT + file LICENSE MD5sum: fb7a4a05b0e49f82d4b4b784649a12fc Package: progeny Version: 1.26.0 Depends: R (>= 3.6.0) Imports: Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2 Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) License: Apache License (== 2.0) | file LICENSE MD5sum: 9c5d81931d29eef0223628f9c8a0815c Package: projectR Version: 1.20.0 Depends: R (>= 4.0.0) Imports: methods, cluster, stats, limma, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2, viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2, cowplot, ggrepel, umap, tsne Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject License: GPL (== 2) MD5sum: dd907183c53378a3107eb1a39c4354ef Package: pRoloc Version: 1.44.1 Depends: R (>= 3.5), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick License: GPL-2 MD5sum: 65ddaea03a33650b94ecff1e020f1fd0 Package: pRolocGUI Version: 2.14.0 Depends: methods, R (>= 3.1.0), pRoloc (>= 1.27.6), Biobase, MSnbase (>= 2.1.11) Imports: shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics, utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker, shinyhelper, shinyWidgets, shinyjs, colorspace, stats, grDevices, grid, BiocGenerics, shinydashboard Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) License: GPL-2 MD5sum: 3233087dbec8e025263e6eeff831ece2 Package: PROMISE Version: 1.56.0 Depends: R (>= 3.1.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) MD5sum: 3c8600e1c84f33d2bc00993202aa7733 Package: PROPER Version: 1.36.0 Depends: R (>= 3.3) Imports: edgeR Suggests: BiocStyle,DESeq2,DSS,knitr License: GPL MD5sum: 7fc76a043462d3064a4e3e36edbcd524 Package: PROPS Version: 1.26.0 Imports: bnlearn, reshape2, sva, stats, utils, Biobase Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 64e2277a62af6cc3b8709e0f77d475cf Package: Prostar Version: 1.36.2 Depends: R (>= 4.4.0) Imports: DAPAR (>= 1.36.2), DAPARdata (>= 1.34.0), rhandsontable, data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets, webshot, shinythemes, later, shinycssloaders, future, promises, shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase, DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown, rclipboard, sass, shinyTree, shinyWidgets Suggests: BiocStyle, BiocManager, testthat, knitr License: Artistic-2.0 MD5sum: 86972df5e8b2c09482fca80a7d7c4564 Package: proteasy Version: 1.6.0 Depends: R (>= 4.2.0) Imports: data.table, stringr, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v79, Rcpi, methods, utils Suggests: BiocStyle, knitr, rmarkdown, igraph, ComplexHeatmap, viridis, License: GPL-3 MD5sum: ce2ac42620a5bd89bac8726c00e97d6e Package: proteinProfiles Version: 1.44.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 MD5sum: f933b27cdf74fe7eb4b6a4eaa0752020 Package: ProteoDisco Version: 1.10.0 Depends: R (>= 4.1.0), Imports: BiocGenerics (>= 0.38.0), BiocParallel (>= 1.26.0), Biostrings (>= 2.60.1), checkmate (>= 2.0.0), cleaver (>= 1.30.0), dplyr (>= 1.0.6), GenomeInfoDb (>= 1.28.0), GenomicFeatures (>= 1.44.0), GenomicRanges (>= 1.44.0), IRanges (>= 2.26.0), methods (>= 4.1.0), ParallelLogger (>= 2.0.1), plyr (>= 1.8.6), rlang (>= 0.4.11), S4Vectors (>= 0.30.0), tibble (>= 3.1.2), tidyr (>= 1.1.3), VariantAnnotation (>= 1.36.0), XVector (>= 0.32.0), Suggests: AnnotationDbi (>= 1.54.1), BSgenome (>= 1.60.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BiocStyle (>= 2.20.1), DelayedArray (>= 0.18.0), devtools (>= 2.4.2), knitr (>= 1.33), matrixStats (>= 0.59.0), markdown (>= 1.1), org.Hs.eg.db (>= 3.13.0), purrr (>= 0.3.4), RCurl (>= 1.98.1.3), readr (>= 1.4.0), ggplot2 (>= 3.3.5), rmarkdown (>= 2.9), rtracklayer (>= 1.52.0), seqinr (>= 4.2.8), stringr (>= 1.4.0), reshape2 (>= 1.4.4), scales (>= 1.1.1), testthat (>= 3.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2) License: GPL-3 MD5sum: d7631e172c4058457fd10467db19ce53 Package: ProteoMM Version: 1.22.0 Depends: R (>= 3.5) Imports: gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics Suggests: BiocStyle, knitr, rmarkdown License: MIT MD5sum: 64a8221565288568ea44f2adca4fd14a Package: protGear Version: 1.8.0 Depends: R (>= 4.2), dplyr (>= 0.8.0) , limma (>= 3.40.2) ,vsn (>= 3.54.0) Imports: magrittr (>= 1.5) , stats (>= 3.6) , ggplot2 (>= 3.3.0) , tidyr (>= 1.1.3) , data.table (>= 1.14.0), ggpubr (>= 0.4.0), gtools (>= 3.8.2) , tibble (>= 3.1.0) , rmarkdown (>= 2.9) , knitr (>= 1.33), utils (>= 3.6), genefilter (>= 1.74.0), readr (>= 2.0.1) , Biobase (>= 2.52.0), plyr (>= 1.8.6) , Kendall (>= 2.2) , shiny (>= 1.0.0) , purrr (>= 0.3.4), plotly (>= 4.9.0) , MASS (>= 7.3) , htmltools (>= 0.4.0) , flexdashboard (>= 0.5.2) , shinydashboard (>= 0.7.1) , GGally (>= 2.1.2) , pheatmap (>= 1.0.12) , grid(>= 4.1.1), styler (>= 1.6.1) , factoextra (>= 1.0.7) ,FactoMineR (>= 2.4) , rlang (>= 0.4.11), remotes (>= 2.4.0) Suggests: gridExtra (>= 2.3), png (>= 0.1-7) , magick (>= 2.7.3) , ggplotify (>= 0.1.0) , scales (>= 1.1.1) , shinythemes (>= 1.2.0) , shinyjs (>= 2.0.0) , shinyWidgets (>= 0.6.2) , shinycssloaders (>= 1.0.0) , shinyalert (>= 3.0.0) , shinyFiles (>= 0.9.1) , shinyFeedback (>= 0.3.0) License: GPL-3 MD5sum: df055be0dafdb0902bbbc161e7c180eb Package: ProtGenerics Version: 1.36.0 Depends: methods Suggests: testthat License: Artistic-2.0 MD5sum: e43e46ea2fc9ba67b21ac95e7387a75b Package: PSEA Version: 1.38.0 Imports: Biobase, MASS Suggests: BiocStyle License: Artistic-2.0 MD5sum: 5558268d259d24eda3726c57147b4929 Package: psichomics Version: 1.30.0 Depends: R (>= 4.0), shiny (>= 1.7.0), shinyBS Imports: AnnotationDbi, AnnotationHub, BiocFileCache, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods LinkingTo: Rcpp Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling License: MIT + file LICENSE MD5sum: f43d18db295573f480b065a0e1e0ef35 Package: PSMatch Version: 1.8.0 Depends: S4Vectors Imports: utils, stats, igraph, methods, Matrix, BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1), QFeatures, MsCoreUtils Suggests: msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat License: Artistic-2.0 MD5sum: f04a14284f0325330191d93013b496b3 Package: psygenet2r Version: 1.36.0 Depends: R (>= 3.4) Imports: stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel, biomaRt, BgeeDB, topGO, Biobase, labeling, GO.db Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: ceb4af869285a5f0218e1270c165c170 Package: puma Version: 3.46.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL MD5sum: 5927241f0d64df19e501a239c06ad507 Package: PureCN Version: 2.10.0 Depends: R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat Enhances: genomicsdb (>= 0.0.3) License: Artistic-2.0 MD5sum: 1e2ba57520217ca17118ace6859b9167 Package: pvac Version: 1.52.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: 1d45e9d198d38309eef9600821576683 Package: pvca Version: 1.44.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: c03cc943dac6ee63f5392f4076e3c7c7 Package: Pviz Version: 1.38.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: bfddfb15681f5cb7e1e4e7b337c01dfb Package: pwalign Version: 1.0.0 Depends: BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5) Imports: methods, utils LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit Enhances: Rmpi License: Artistic-2.0 MD5sum: fb3a375806fed2255ab5729036ce9707 Package: PWMEnrich Version: 4.40.0 Depends: R (>= 3.5.0), methods, BiocGenerics, Biostrings Imports: grid, seqLogo, gdata, evd, S4Vectors Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 6c71ea1fb3bee3b061d88b4b67c2fa32 Package: pwOmics Version: 1.36.0 Depends: R (>= 3.2) Imports: data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots, Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub, GenomicRanges, graph, grDevices, stats, utils Suggests: ebdbNet, longitudinal, Mfuzz, RUnit License: GPL (>= 2) MD5sum: c8bf80576bb770aa2e972fcc448b7c5c Package: qckitfastq Version: 1.20.0 Imports: magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table, reshape2, grDevices, graphics, stats, utils, Rcpp, rlang, RSeqAn LinkingTo: Rcpp, RSeqAn Suggests: knitr, rmarkdown, kableExtra, testthat License: Artistic-2.0 MD5sum: 53e5b2a30e3fdc5dd856044729da610b Package: qcmetrics Version: 1.42.0 Depends: R (>= 3.3) Imports: Biobase, methods, knitr, tools, xtable, pander, S4Vectors Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown, markdown License: GPL-2 MD5sum: fdbac0d455dff8dea866db5a86f901ba Package: QDNAseq Version: 1.40.0 Depends: R (>= 3.1.0) Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply (>= 1.8.1) Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10 License: GPL MD5sum: 40ac429e3068ae36eef1cf7467eb29fd Package: QFeatures Version: 1.14.2 Depends: R (>= 4.0), MultiAssayExperiment Imports: methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics, ProtGenerics (>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils (>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect, reshape2 Suggests: SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap License: Artistic-2.0 MD5sum: 33183ddf97d7858470ac114e0add596e Package: qmtools Version: 1.8.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics, limma Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 1875ef4e36ea7ddfaa9cd2042ca6ba72 Package: qpcrNorm Version: 1.62.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) MD5sum: ac5ac379d593c92399eef016556d5565 Package: qpgraph Version: 2.38.0 Depends: R (>= 3.5) Imports: methods, parallel, Matrix (>= 1.5-0), grid, annotate, graph (>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats License: GPL (>= 2) MD5sum: 487c55f90d0ee9e40f1c3161b65692b1 Package: qPLEXanalyzer Version: 1.22.0 Depends: R (>= 4.0), Biobase, MSnbase Imports: assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0), ggdendro, ggplot2, graphics, grDevices, IRanges, limma, magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang, scales, stats, stringr, tibble, tidyr, tidyselect, utils Suggests: gridExtra, knitr, qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr License: GPL-2 MD5sum: 9c71edc77085ccb7cb27659cf3303572 Package: qsea Version: 1.30.0 Depends: R (>= 4.3) Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS License: GPL-2 MD5sum: 74c89d0f38d87467d733a62458a6bf7c Package: qsmooth Version: 1.20.0 Depends: R (>= 4.0) Imports: SummarizedExperiment, utils, sva, stats, methods, graphics, Hmisc Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 3560f9e44eb3943ab35da514bff2ddd8 Package: QSutils Version: 1.22.0 Depends: R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods Imports: ape, stats, psych Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL-2 MD5sum: f0864d83d4e899844493c5487121db5d Package: qsvaR Version: 1.8.0 Depends: R (>= 4.2), SummarizedExperiment Imports: sva, stats, ggplot2, methods Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5c2eccd3f343764dcf3ce4e9b109c796 Package: QTLExperiment Version: 1.2.0 Depends: SummarizedExperiment Imports: methods, rlang, checkmate, dplyr, collapse, vroom, tidyr, tibble, utils, stats, ashr, S4Vectors, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, covr License: GPL-3 MD5sum: ac98611c6855705ec9e4f636abbdcb98 Package: Qtlizer Version: 1.18.0 Depends: R (>= 3.6.0) Imports: httr, curl, GenomicRanges, stringi Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 8886dacb4b84097ee27eee3d5a07379d Package: quantiseqr Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils Suggests: AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble License: GPL-3 MD5sum: db44b79c42074d05d8a59463bc9b0275 Package: quantro Version: 1.38.0 Depends: R (>= 4.0) Imports: Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer Suggests: rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: f09c34d5479fb23270522a83dc42eb8a Package: quantsmooth Version: 1.70.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 MD5sum: 7e571148e5b00465f20fa4cc8b5aeb40 Package: QuasR Version: 1.44.0 Depends: R (>= 4.4), parallel, GenomicRanges, Rbowtie Imports: methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools (>= 2.13.1), GenomicFeatures, txdbmaker, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi LinkingTo: Rhtslib (>= 1.99.1) Suggests: Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 MD5sum: dc8e0788fffb8f8b2fca7de9169dbe43 Package: QuaternaryProd Version: 1.38.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) LinkingTo: Rcpp Suggests: knitr License: GPL (>= 3) MD5sum: c27b1786662bc60742af006e6775b45e Package: QUBIC Version: 1.32.0 Depends: R (>= 3.1), biclust Imports: Rcpp (>= 0.11.0), methods, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown Enhances: RColorBrewer License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: a601e92918465c14fff8873eda079767 Package: qusage Version: 2.38.0 Depends: R (>= 2.10), limma (>= 3.14), methods Imports: utils, Biobase, nlme, emmeans, fftw License: GPL (>= 2) MD5sum: fdaa2682900959e25daf2f16a834d5d9 Package: qvalue Version: 2.36.0 Depends: R(>= 2.10) Imports: splines, ggplot2, grid, reshape2 Suggests: knitr License: LGPL MD5sum: 0319abe946da487705ffe1af5d6ddcad Package: r3Cseq Version: 1.50.0 Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked License: GPL-3 MD5sum: bea2da2de5ecb5ba6d651f977c983505 Package: R453Plus1Toolbox Version: 1.54.0 Depends: R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), pwalign, Biobase Imports: utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector, GenomicRanges (>= 1.31.8), SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools, ShortRead (>= 1.37.1) Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 License: LGPL-3 MD5sum: 793dc96a8d79d3c6a53f97d6854b9b1b Package: R4RNA Version: 1.32.0 Depends: R (>= 3.2.0), Biostrings (>= 2.38.0) License: GPL-3 MD5sum: b74537953bc7893cfbfba9aecadf333a Package: RadioGx Version: 2.8.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, data.table, S4Vectors, Biobase, parallel, BiocParallel, RColorBrewer, caTools, magicaxis, methods, reshape2, scales, grDevices, graphics, stats, utils, assertthat, matrixStats, downloader Suggests: rmarkdown, BiocStyle, knitr, pander, markdown License: GPL-3 MD5sum: b7d0ad756ec84aba4975800f83d36463 Package: raer Version: 1.2.0 Imports: stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, GenomeInfoDb, GenomicAlignments, GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer, Matrix, cli LinkingTo: Rhtslib Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata, txdbmaker License: MIT + file LICENSE MD5sum: 7450ca5da754fabeca5e2d3afa491494 Package: RaggedExperiment Version: 1.28.0 Depends: R (>= 4.2.0), GenomicRanges (>= 1.37.17) Imports: BiocBaseUtils, BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment License: Artistic-2.0 MD5sum: 178fbec2b632078236f7a50cf29c0edb Package: RAIDS Version: 1.2.0 Depends: R (>= 4.2.0), gdsfmt, SNPRelate, stats, utils, GENESIS Imports: S4Vectors, GenomicRanges, ensembldb, BSgenome, AnnotationDbi, methods, class, pROC, IRanges, AnnotationFilter, rlang, VariantAnnotation, MatrixGenerics, Suggests: testthat, knitr, rmarkdown, BiocStyle, withr, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: Apache License (>= 2) MD5sum: 52740bb40c3050b41578a9a1004a263b Package: rain Version: 1.38.0 Depends: R (>= 2.10), gmp, multtest Suggests: lattice, BiocStyle License: GPL-2 MD5sum: a65397d27ec25cd03ad27d1b2c5bc8c6 Package: ramr Version: 1.12.0 Depends: R (>= 4.1), GenomicRanges, parallel, doParallel, foreach, doRNG, methods Imports: IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist, matrixStats, S4Vectors Suggests: RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 4ae750265015a670c7c2a27e1a212103 Package: ramwas Version: 1.28.0 Depends: R (>= 3.3.0), methods, filematrix Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 MD5sum: 8916857eb438d3762c64195ec2b931e6 Package: randPack Version: 1.50.0 Depends: methods Imports: Biobase License: Artistic-2.0 MD5sum: b1cd36a4e19c1a4916a4e9676109c799 Package: RankProd Version: 3.30.0 Depends: R (>= 3.2.1), stats, methods, Rmpfr, gmp Imports: graphics License: file LICENSE License_restricts_use: yes MD5sum: de97696eae243f5832f2b3a26419286d Package: RAREsim Version: 1.8.0 Depends: R (>= 4.1.0) Imports: nloptr Suggests: markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 0f9efcb810da1245484361d77b86102c Package: RareVariantVis Version: 2.32.0 Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores Suggests: knitr License: Artistic-2.0 MD5sum: 37fb0ee2fd098593e838918d8a56c725 Package: Rarr Version: 1.4.0 Imports: jsonlite, httr, stringr, R.utils, utils, paws.storage, methods Suggests: BiocStyle, covr, knitr, tinytest, mockery License: MIT + file LICENSE MD5sum: 0fe75493bb999685bc5dae04aa534f74 Package: rawDiag Version: 1.0.0 Depends: R (>= 4.3) Imports: dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools, BiocManager, BiocParallel, rawrr (>= 1.10), rlang, reshape2, scales, shiny (>= 1.5), stats, utils Suggests: BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat License: GPL-3 MD5sum: 45fc35af4da259f9cbc37dfd1008eafc Package: rawrr Version: 1.12.0 Depends: R (>= 4.1) Imports: grDevices, graphics, stats, utils Suggests: BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: fc9bb73618697b5f542d7f90bc31146b Package: RbcBook1 Version: 1.72.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 MD5sum: 3a867c4127763161239827c13933d842 Package: RBGL Version: 1.80.0 Depends: graph, methods Imports: methods LinkingTo: BH Suggests: Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 2d9bfb9b53b269c03bd571096a7f5dd2 Package: RBioFormats Version: 1.4.0 Imports: EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats Suggests: BiocStyle, knitr, testthat, xml2 License: GPL-3 MD5sum: 22cad67b37248065de1ee04296769210 Package: RBioinf Version: 1.64.0 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 MD5sum: f14a4895410e3de261fc3621caca38b8 Package: rBiopaxParser Version: 2.44.0 Depends: R (>= 4.0), data.table Imports: XML Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph License: GPL (>= 2) MD5sum: d40450cfacde0b56243877ef0eb3257a Package: rBLAST Version: 1.0.0 Depends: Biostrings (>= 2.26.2) Imports: methods, utils, BiocFileCache Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: e5069c963d5de10bc0e02ad71f735b33 Package: RBM Version: 1.36.0 Depends: R (>= 3.2.0), limma, marray License: GPL (>= 2) MD5sum: 48477726796b8587d3d281626022bdf9 Package: Rbowtie Version: 1.44.0 Imports: utils Suggests: testthat, parallel, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | file LICENSE Archs: x64 MD5sum: 8c2c3bac7b2385be58f5e8dc67bd271b Package: Rbowtie2 Version: 2.10.0 Depends: R (>= 4.1.0) Imports: magrittr, Rsamtools Suggests: knitr, testthat (>= 3.0.0), rmarkdown License: GPL (>= 3) Archs: x64 MD5sum: 93d1c98841f85e55133e3bbc146670c2 Package: rbsurv Version: 2.62.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) MD5sum: 90bb9f060600fec6be9e8606ec8664a7 Package: Rbwa Version: 1.8.0 Depends: R (>= 4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE OS_type: unix MD5sum: 5b59c263a4af989be207d40b83e5e930 Package: RCAS Version: 1.30.0 Depends: R (>= 3.5.0), plotly (>= 4.5.2), DT (>= 0.2), data.table Imports: GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer, GenomicFeatures, txdbmaker, rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors, plotrix, pbapply, RSQLite, proxy, pheatmap, ggplot2, cowplot, seqLogo, utils, ranger, gprofiler2 Suggests: testthat, covr, BiocManager License: Artistic-2.0 MD5sum: 9d73516adfb5d188818125d24bdd523a Package: RCASPAR Version: 1.50.0 License: GPL (>= 3) MD5sum: 5945d9629ecc37428a0af2c2d541ade1 Package: rcellminer Version: 2.26.0 Depends: R (>= 3.2), Biobase, rcellminerData (>= 2.0.0) Imports: stringr, gplots, ggplot2, methods, stats, utils, shiny Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown License: LGPL-3 + file LICENSE MD5sum: fd702f1491e614dfdf6bf491a7cd41b9 Package: rCGH Version: 1.34.0 Depends: R (>= 3.4),methods,stats,utils,graphics Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1), limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi, parallel,IRanges,grDevices,aCGH Suggests: BiocStyle, knitr, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 2e6c7bd376107315accb4c35d08613ee Package: RcisTarget Version: 1.24.0 Depends: R (>= 3.5.0) Imports: AUCell (>= 1.1.6), BiocGenerics, data.table, graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble, GSEABase, methods, R.utils, stats, SummarizedExperiment, S4Vectors, utils, zoo Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork Enhances: doMC, doRNG License: GPL-3 MD5sum: f31b6c8b0fc52cf0cb0b40960f40aa95 Package: RCM Version: 1.20.0 Depends: R (>= 4.0), DBI Imports: RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM, ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS, grDevices, graphics, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: bbbb352aee6cf7e6ca7077df24a0b0f9 Package: Rcpi Version: 1.40.0 Depends: R (>= 3.0.2) Imports: Biostrings, GOSemSim, RCurl, doParallel, foreach, methods, pwalign, rjson, rlang, stats, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 | file LICENSE MD5sum: a9ed411fbac2715429babf7d7b9c0496 Package: RCSL Version: 1.12.0 Depends: R (>= 4.1) Imports: RcppAnnoy, igraph, NbClust, Rtsne, ggplot2(>= 3.4.0), methods, pracma, umap, grDevices, graphics, stats, Rcpp (>= 0.11.0), MatrixGenerics, SingleCellExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown, mclust, tidyverse, tinytex License: Artistic-2.0 MD5sum: 8ed0dc1bb8578e69f33d875bfb73a25e Package: Rcwl Version: 1.20.0 Depends: R (>= 3.6), yaml, methods, S4Vectors Imports: utils, stats, BiocParallel, batchtools, DiagrammeR, shiny, R.utils, codetools, basilisk Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: a3354e19b9543ade70281f5ed8c70df8 Package: RcwlPipelines Version: 1.20.0 Depends: R (>= 3.6), Rcwl, BiocFileCache Imports: rappdirs, methods, utils, git2r, httr, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 38ade33f1b80c1a655a520eb72a4a55a Package: RCX Version: 1.8.0 Depends: R (>= 4.2.0) Imports: jsonlite, plyr, igraph, methods Suggests: BiocStyle, testthat, knitr, rmarkdown, base64enc, graph License: MIT + file LICENSE MD5sum: 29665431457db02b183bdfcd632f0bfc Package: RCy3 Version: 2.24.0 Imports: httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots Suggests: BiocStyle, knitr, rmarkdown, igraph, grDevices License: MIT + file LICENSE MD5sum: e57ad6eea92e9134e646c946a1c90add Package: RCyjs Version: 2.26.1 Depends: R (>= 3.5.0), BrowserViz (>= 2.7.18), graph (>= 1.56.0) Imports: methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 77003a3506fde0baefe1167d2947589f Package: rDGIdb Version: 1.30.0 Imports: jsonlite,httr,methods,graphics Suggests: BiocStyle,knitr,testthat License: MIT + file LICENSE MD5sum: bc0989a91fa3c98965dc2905538957bb Package: Rdisop Version: 1.64.0 Depends: R (>= 2.0.0), Rcpp LinkingTo: Rcpp Suggests: RUnit License: GPL-2 MD5sum: 8d44c9f82ac0cbe17d646e2e082ac34c Package: RDRToolbox Version: 1.54.0 Depends: R (>= 2.9.0) Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) MD5sum: 94ca5da7a94b0092c0132dd398e506fe Package: ReactomeContentService4R Version: 1.12.0 Imports: httr, jsonlite, utils, magick (>= 2.5.1), data.table, doParallel, foreach, parallel Suggests: pdftools, testthat, knitr, rmarkdown License: Apache License (>= 2.0) | file LICENSE MD5sum: bc776faa7f271756dc750f2870721001 Package: ReactomeGraph4R Version: 1.12.0 Depends: R (>= 4.1) Imports: neo4r, utils, getPass, jsonlite, purrr, magrittr, data.table, rlang, ReactomeContentService4R, doParallel, parallel, foreach Suggests: knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson License: Apache License (>= 2) MD5sum: 915cfbc7b7bcfdb4bcb0845d3f1c0497 Package: ReactomeGSA Version: 1.18.0 Imports: jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer, dplyr, tidyr, Biobase Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, devtools Enhances: limma, edgeR, Seurat (>= 3.0), scater License: MIT + file LICENSE MD5sum: 7187461603736ecca6c4685d7541d0e2 Package: ReactomePA Version: 1.48.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2 (>= 3.3.5), ggraph, reactome.db, igraph, graphite, gson Suggests: BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat License: GPL-2 MD5sum: 360c4a87c2dd7ff5387ae065fc22d9fe Package: ReadqPCR Version: 1.50.0 Depends: R(>= 2.14.0), Biobase, methods Suggests: qpcR License: LGPL-3 MD5sum: 78659bf093ecbbbb57461c6e8576bafe Package: REBET Version: 1.22.0 Depends: ASSET Imports: stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 700a990f6f6d12ec03a83a31c5f73cbc Package: rebook Version: 1.14.0 Imports: utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends, dir.expiry, filelock, BiocStyle Suggests: testthat, igraph, XML, BiocManager, RCurl, bookdown, rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows License: GPL-3 MD5sum: 214a033fdbea0bc74bebcee6bbce189e Package: receptLoss Version: 1.16.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 2.1.0), here License: GPL-3 + file LICENSE MD5sum: c1da03aaa767c6cb766e13422b885704 Package: reconsi Version: 1.16.0 Imports: phyloseq, ks, reshape2, ggplot2, stats, methods, graphics, grDevices, matrixStats, Matrix Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: d607a26daafdc2063d201c7784131a51 Package: recount Version: 1.30.2 Depends: R (>= 3.5.0), SummarizedExperiment Imports: BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer (>= 1.35.3), S4Vectors, stats, utils Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, txdbmaker, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer License: Artistic-2.0 MD5sum: e83344da67e50669bc44f23f68f81c16 Package: recount3 Version: 1.14.0 Depends: SummarizedExperiment Imports: BiocFileCache, methods, rtracklayer, S4Vectors, utils, httr, data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools Suggests: BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount License: Artistic-2.0 MD5sum: 5778ce19e9f50c565e962257f8f46339 Package: recountmethylation Version: 1.14.0 Depends: R (>= 4.1) Imports: minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats Suggests: minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub License: Artistic-2.0 MD5sum: 3e5beb0046be11b36bb653e6b5f0287b Package: recoup Version: 1.32.0 Depends: R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap Imports: BiocGenerics, biomaRt, Biostrings, circlize, GenomeInfoDb, GenomicFeatures, graphics, grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, txdbmaker, utils Suggests: grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL License: GPL (>= 3) MD5sum: cf9e3b1575f7e73a96e9d6c6e9bcc707 Package: RedeR Version: 3.0.0 Depends: R (>= 4.0), methods Imports: scales, igraph Suggests: knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf License: GPL-3 MD5sum: b40eaf4d15a51635852952a6cd801ae3 Package: RedisParam Version: 1.6.0 Depends: R (>= 4.2.0), BiocParallel (>= 1.29.12) Imports: methods, redux, withr, futile.logger Suggests: rmarkdown, knitr, testthat, BiocStyle License: Artistic-2.0 MD5sum: 11f988fe7cbc3c9948c9866ff7186215 Package: REDseq Version: 1.50.0 Depends: R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils License: GPL (>= 2) MD5sum: 290c1639158cef64626a3bad8470ffa6 Package: RefPlus Version: 1.74.0 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) MD5sum: c38995e154269638cda29ee2d2d5b254 Package: RegEnrich Version: 1.14.0 Depends: R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet, SummarizedExperiment Imports: randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA, ggplot2 (>= 2.2.0), methods, reshape2, magrittr, BiocStyle Suggests: GEOquery, rmarkdown, knitr, BiocManager, testthat License: GPL (>= 2) MD5sum: 91b78a56ce053ba7f0cb763a3f031fd3 Package: regionalpcs Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr, PCAtools, tibble, GenomicRanges Suggests: knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges License: MIT + file LICENSE MD5sum: 8012cb03c24366c58eb47ab7e6d885b6 Package: RegionalST Version: 1.2.0 Depends: R (>= 4.3.0) Imports: stats, grDevices, utils, ggplot2, dplyr, scater, gridExtra, BayesSpace, fgsea, magrittr, SingleCellExperiment, RColorBrewer, Seurat, S4Vectors, tibble, TOAST, assertthat, colorspace, shiny, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, gplots, testthat (>= 3.0.0) License: GPL-3 MD5sum: 62e1b2e0f6ee5d569efebe601c9f7ead Package: regioneR Version: 1.36.0 Depends: GenomicRanges Imports: memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, S4Vectors, tools Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat License: Artistic-2.0 MD5sum: d5b29df3864ed98dc388b5d6cc8f4ee5 Package: regioneReloaded Version: 1.6.0 Depends: R (>= 4.2), regioneR Imports: stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2, methods, scales, cluster, grid, grDevices Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 023aef9d6c41c6dbafa03d5e67694d27 Package: regionReport Version: 1.38.0 Depends: R(>= 3.2) Imports: BiocStyle (>= 2.5.19), derfinder (>= 1.25.3), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker License: Artistic-2.0 MD5sum: 81cdb0f9684fe561f8e0fd50467da557 Package: regsplice Version: 1.30.0 Imports: glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a462b5eff4776dbc4640b6a4fadccf38 Package: regutools Version: 1.16.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges, Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils, BiocFileCache Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: b0fc70dca06aaa720dff47624fb50ecd Package: REMP Version: 1.28.0 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: 0e6f0fa622385edad06ec00d4a41b06d Package: Repitools Version: 1.50.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.8.0) Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Rsolnp, cluster Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) MD5sum: 3f755162986154d017f81e59c687a806 Package: ReportingTools Version: 2.44.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown License: Artistic-2.0 MD5sum: a8a8bff0fa944613041dc5f6e0528597 Package: RepViz Version: 1.20.0 Depends: R (>= 3.5.1), GenomicRanges (>= 1.30.0), Rsamtools (>= 1.34.1), IRanges (>= 2.14.0), biomaRt (>= 2.36.0), S4Vectors (>= 0.18.0), graphics, grDevices, utils Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: 24eaba21fb5306a5e95dac76996fd8ca Package: ResidualMatrix Version: 1.14.1 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: 2f3deeb9bd82ece821a7751c0aac9d41 Package: RESOLVE Version: 1.6.0 Depends: R (>= 4.1.0) Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel, reshape2, S4Vectors Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: ca2b287accd6c2ca898df46b8d75b40e Package: retrofit Version: 1.4.0 Depends: R (>= 4.2), Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl License: GPL-3 MD5sum: 70cd63e67d392f8fcd0e69698781d4a9 Package: ReUseData Version: 1.4.0 Imports: Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools, utils, methods, jsonlite, yaml, basilisk Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 31246e1d8948b40f6b52b18453d7e3f7 Package: rexposome Version: 1.26.0 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, ggridges, reshape2, pryr, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown License: MIT + file LICENSE MD5sum: 675f7cf07a31dad8609258d1fcc966ab Package: rfaRm Version: 1.16.0 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors, jsonlite Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit License: GPL-3 MD5sum: 231c96d02d58b05cf83ef5f59fecd48a Package: Rfastp Version: 1.14.0 Imports: Rcpp, rjson, ggplot2, reshape2 LinkingTo: Rcpp, Rhtslib, zlibbioc Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: b292950e014b2f1b5b817b9d619cfd5d Package: rfPred Version: 1.42.0 Depends: R (>= 3.5.0), methods Imports: utils, GenomeInfoDb, data.table, IRanges, GenomicRanges, parallel, Rsamtools Suggests: BiocStyle License: GPL (>= 2) MD5sum: ad5aa7bd0dd996637924fe255863c379 Package: rGADEM Version: 2.52.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, GenomicRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer License: Artistic-2.0 MD5sum: 0027fc005095d55db3dc41111533e165 Package: rGenomeTracks Version: 1.10.0 Depends: R (>= 4.1.0), Imports: imager, reticulate, methods, rGenomeTracksData Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: ee6aa00cedc1738184f22510d6438614 Package: RgnTX Version: 1.6.0 Depends: R (>= 4.2.0) Imports: GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, IRanges, methods, regioneR, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 86c6549398d31137057819ce228dd4be Package: rgoslin Version: 1.8.0 Imports: Rcpp (>= 1.0.3), dplyr LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr License: MIT + file LICENSE MD5sum: 0c9dda0e66be1ab26dfc4ad9c8d16007 Package: RGraph2js Version: 1.32.0 Imports: utils, whisker, rjson, digest, graph Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna License: GPL-2 MD5sum: 43d7248bcce4c61cc72cf6e269c32f3e Package: Rgraphviz Version: 2.48.0 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL MD5sum: 6457db3ab63dddc960e6ce5b347d7bef Package: rGREAT Version: 2.6.0 Depends: R (>= 4.0.0), GenomicRanges, IRanges, methods Imports: graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats, GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db, progress, circlize, AnnotationDbi, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db Enhances: BioMartGOGeneSets, UniProtKeywords License: MIT + file LICENSE MD5sum: cf2c3fc79636c87f5c65ab452c0b03ea Package: RGSEA Version: 1.38.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) MD5sum: 11b54c59883b57c5ade436af82bc8d26 Package: rgsepd Version: 1.36.0 Depends: R (>= 4.2.0), DESeq2, goseq (>= 1.28) Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi Suggests: boot, tools, BiocGenerics, knitr, xtable License: GPL-3 MD5sum: 699f45f46b1a285411aad0e750e7527b Package: rhdf5 Version: 2.48.0 Depends: R (>= 4.0.0), methods Imports: Rhdf5lib (>= 1.13.4), rhdf5filters (>= 1.15.5) LinkingTo: Rhdf5lib Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel License: Artistic-2.0 MD5sum: 7df2498ca51d820dfc040d3e1f7d1cf3 Package: rhdf5client Version: 1.26.0 Depends: R (>= 3.6), methods, DelayedArray Imports: httr, rjson, utils, data.table Suggests: knitr, testthat, BiocStyle, DT, rmarkdown License: Artistic-2.0 MD5sum: 9df8f60ad9ecc417008b3f63638710f3 Package: rhdf5filters Version: 1.16.0 LinkingTo: Rhdf5lib Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7) License: BSD_2_clause + file LICENSE MD5sum: 23f31a98093c65f757c4b70f58d8098d Package: Rhdf5lib Version: 1.26.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery License: Artistic-2.0 MD5sum: 39b58cc7e66f9f68dda2f9dd4fd1c07f Package: Rhisat2 Version: 1.20.0 Depends: R (>= 4.4.0) Imports: txdbmaker, SGSeq, GenomicRanges, methods, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 MD5sum: f16ea58d3e5248e9113705b4f04e9cdd Package: Rhtslib Version: 3.0.0 Imports: tools, zlibbioc LinkingTo: zlibbioc Suggests: knitr, rmarkdown, BiocStyle License: LGPL (>= 2) MD5sum: 646b420e295456fcfd4b270f1585f12a Package: RiboCrypt Version: 1.10.0 Depends: R (>= 3.6.0), ORFik (>= 1.13.12) Imports: bslib, BiocGenerics, BiocParallel, Biostrings, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, httr, IRanges, jsonlite, knitr, markdown, NGLVieweR, plotly, rlang, RCurl, shiny, shinycssloaders, shinyhelper, shinyjqui, stringr Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: c125bf6bc5d49c20b3aad34ece1d4562 Package: RiboDiPA Version: 1.12.0 Depends: R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache, BiocGenerics, txdbmaker LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 114af8448f8a11b3cb85dcc5d1c1222c Package: RiboProfiling Version: 1.34.0 Depends: R (>= 3.5.0), Biostrings Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: 588d2b3f79e7f8c813b1011664a5e32a Package: ribor Version: 1.16.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: d95f26d0722a11f696000495dde51ebc Package: riboSeqR Version: 1.38.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, S4Vectors, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: 7c781902afb579dfd9c6192886a7e94c Package: ribosomeProfilingQC Version: 1.16.0 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid, txdbmaker, ggExtra Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase License: GPL (>= 3) + file LICENSE MD5sum: 678d20a37624723f5efc3c08f035c8a2 Package: rifi Version: 1.8.0 Depends: R (>= 4.2) Imports: car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 207ab685c96c5f113137808fd14846ef Package: rifiComparative Version: 1.4.0 Depends: R (>= 4.2) Imports: cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, ggrepel, graphics, grDevices, grid, methods, nnet, rlang, S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils, writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment Suggests: DescTools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 4106ace76ebd44a8486b3a2940681816 Package: RImmPort Version: 1.32.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 8fc49ec9f908493ad4bccddef45057e8 Package: RIPAT Version: 1.14.0 Depends: R (>= 4.0) Imports: biomaRt (>= 2.38.0), GenomicRanges (>= 1.34.0), ggplot2 (>= 3.1.0), grDevices (>= 3.5.3), IRanges (>= 2.16.0), karyoploteR (>= 1.6.3), openxlsx (>= 4.1.4), plyr (>= 1.8.4), regioneR (>= 1.12.0), rtracklayer (>= 1.42.2), stats (>= 3.5.3), stringr (>= 1.3.1), utils (>= 3.5.3) Suggests: knitr (>= 1.28) License: Artistic-2.0 MD5sum: f4a0e84c7e422039b2a55a7f274daa97 Package: RITAN Version: 1.28.0 Depends: R (>= 4.0), Imports: graphics, methods, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86 Suggests: rmarkdown, BgeeDB License: file LICENSE MD5sum: 9d7661c273362832ddcea48c885a7a35 Package: RIVER Version: 1.28.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: a98e78321dc30cc3f062ac6bac8f9d16 Package: RJMCMCNucleosomes Version: 1.28.0 Depends: R (>= 3.5.0), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 MD5sum: 4ade489292d6dfe9057a98b825d26de2 Package: RLassoCox Version: 1.12.0 Depends: R (>= 4.1), glmnet Imports: Matrix, igraph, survival, stats Suggests: knitr License: Artistic-2.0 MD5sum: 3c989a33c60aa7429ded9f7cf8e1d1c8 Package: RLMM Version: 1.66.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: f343f6601f1fcf4c43fb9820b622041a Package: Rmagpie Version: 1.60.0 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) MD5sum: 236660e7ecc251e41f97f676e7eeb22e Package: rmelting Version: 1.20.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.9-8) Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat License: GPL-2 | GPL-3 MD5sum: 9084e4bf37fbc4ee3dadd28c7f975da7 Package: Rmmquant Version: 1.22.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, apeglm, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8741c81df3732b04446f81c77a869831 Package: rmspc Version: 1.10.0 Imports: processx, BiocManager, rtracklayer, stats, tools, methods, GenomicRanges, stringr Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2f0b6a4c661403a96ee6461e2b08b0a0 Package: RNAAgeCalc Version: 1.16.0 Depends: R (>= 3.6) Imports: ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 9fe8c7b5bbf28f116b4b5af94dc4c0b9 Package: RNAdecay Version: 1.24.0 Depends: R (>= 3.5) Imports: stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr, scales Suggests: parallel, knitr, reshape2, rmarkdown License: GPL-2 MD5sum: 4baa237d8ff0a6995c4ccd47247de9a4 Package: rnaEditr Version: 1.14.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb, bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: e649fe389af6b503ab090160e8a59988 Package: RNAinteract Version: 1.52.0 Depends: R (>= 2.12.0), Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12), abind, locfit, Biobase License: Artistic-2.0 MD5sum: bcec2897c0a64b63f18ce4071d05f561 Package: RNAmodR Version: 1.18.0 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomicRanges, Modstrings Imports: methods, stats, grDevices, matrixStats, BiocGenerics, Biostrings (>= 2.57.2), BiocParallel, txdbmaker, GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, ggplot2, Gviz (>= 1.31.0), reshape2, graphics, ROCR Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data License: Artistic-2.0 MD5sum: 9bba1cd51b9a309c9116284bd3eb7a0d Package: RNAmodR.AlkAnilineSeq Version: 1.18.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data License: Artistic-2.0 MD5sum: ce1a6a61099fc8de6b1b018ef96e983f Package: RNAmodR.ML Version: 1.18.0 Depends: R (>= 3.6), RNAmodR Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 MD5sum: 2b8b897de2d3b863ef58731d8451c612 Package: RNAmodR.RiboMethSeq Version: 1.18.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data License: Artistic-2.0 MD5sum: ddb76115604d35b2185f0aa211e05bf1 Package: RNAsense Version: 1.18.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: c246c12196894f65e35735d3f403d93f Package: rnaseqcomp Version: 1.34.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 5d38d13c40ae6032d445edb58247d8b0 Package: RNAseqCovarImpute Version: 1.2.0 Depends: R (>= 4.3.0) Imports: Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr, magrittr, rlang, edgeR, foreach, mice Suggests: BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 91ea8d8c99164cfcf36e96449e63ecad Package: RNASeqPower Version: 1.44.0 License: LGPL (>= 2) MD5sum: 24a92742c171eb142f0e5e0c9a8713d1 Package: RnaSeqSampleSize Version: 2.14.0 Depends: R (>= 4.0.0), ggplot2, RnaSeqSampleSizeData Imports: biomaRt,edgeR,heatmap3,matlab,KEGGREST,methods,grDevices, graphics, stats, Rcpp (>= 0.11.2),recount,ggpubr,SummarizedExperiment,tidyr,dplyr,tidyselect,utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 52352ec1ca894fcc418dd2857800899d Package: RnBeads Version: 2.22.0 Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame License: GPL-3 MD5sum: 63e3b0efd9d7d48d0d23d97f9cb20407 Package: Rnits Version: 1.38.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: 57337b76bbdb4b7243a321e7f102c83b Package: roar Version: 1.40.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 MD5sum: 9c6186412cd99aee0bdfdd6c986d4f2f Package: roastgsa Version: 1.2.0 Depends: R (>= 4.3.0) Imports: parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, limma, Biobase Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 License: GPL-3 MD5sum: 0234c78121af241d8848a4e2540455ca Package: ROC Version: 1.80.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: rmarkdown, Biobase, BiocStyle License: Artistic-2.0 MD5sum: b8e20a90362746e4ba2b576baeb72d7c Package: ROCpAI Version: 1.16.0 Depends: boot, SummarizedExperiment, fission, knitr, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: fa23590af7a032246c3a5032eed8fb02 Package: RolDE Version: 1.8.0 Depends: R (>= 4.2.0) Imports: stats, methods, ROTS, matrixStats, foreach, parallel, doParallel, doRNG, rngtools, SummarizedExperiment, nlme, qvalue, grDevices, graphics, utils Suggests: knitr, printr, rmarkdown, testthat License: GPL-3 MD5sum: 1236a25702e6ba70b5480499f67f824d Package: rols Version: 3.0.0 Depends: methods Imports: httr2, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1) Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, License: GPL-2 MD5sum: e9ca93ed9e7a6116dc3e02caf43dd739 Package: ROntoTools Version: 2.32.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: dfcd8abb212276a01c53969c20a78371 Package: ROSeq Version: 1.16.0 Depends: R (>= 4.0) Imports: pbmcapply, edgeR, limma Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics License: GPL-3 MD5sum: 7d39cd226783765be364417523865147 Package: ROTS Version: 1.32.0 Depends: R (>= 3.3) Imports: Rcpp, stats, Biobase, methods LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: c3a3e514929ee76fbeb5c2a4b87f51fc Package: RPA Version: 1.60.0 Depends: R (>= 3.1.1), affy, BiocGenerics, BiocStyle, methods, rmarkdown Imports: phyloseq Suggests: knitr, parallel License: BSD_2_clause + file LICENSE MD5sum: 990cffb2aa1887a4aa21b72b96e229f5 Package: rprimer Version: 1.8.0 Depends: R (>= 4.1) Imports: Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback Suggests: BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) License: GPL-3 MD5sum: 15d166975ed2615ddf47426a282dc1d0 Package: RProtoBufLib Version: 2.16.0 Suggests: knitr, rmarkdown License: BSD_3_clause MD5sum: 6c6037f91bd99d9cd0d84f0c17266db5 Package: rpx Version: 2.12.0 Depends: R (>= 3.5.0), methods Imports: BiocFileCache, jsonlite, xml2, RCurl, curl, utils Suggests: Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown License: GPL-2 MD5sum: d72844b2cbcb62776aac5470333b1a5b Package: Rqc Version: 1.38.0 Depends: BiocParallel, ShortRead, ggplot2 Imports: BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles LinkingTo: Rcpp Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 43bfffe1fff6528201d8dcf91fc5ca97 Package: rqt Version: 1.30.0 Depends: R (>= 3.4), SummarizedExperiment Imports: stats,Matrix,ropls,methods,car,RUnit,metap,CompQuadForm,glmnet,utils,pls Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: f5c3dce1a4a94db1d6b629ba5f66192b Package: rqubic Version: 1.50.0 Imports: methods, Biobase, BiocGenerics, biclust Suggests: RColorBrewer License: GPL-2 MD5sum: 0ac917fd088741bc1a80eccb914c848b Package: rRDP Version: 1.38.0 Depends: Biostrings (>= 2.26.2) Imports: rJava, utils Suggests: rRDPData, knitr, rmarkdown License: GPL-2 + file LICENSE MD5sum: 49e85d155afdddc0f416a614759c9511 Package: RRHO Version: 1.44.0 Depends: R (>= 2.10), grid Imports: VennDiagram Suggests: lattice License: GPL-2 MD5sum: 7d18cf9d0b6182cfd0c50b640d1c5968 Package: rrvgo Version: 1.16.0 Imports: GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel, treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods, umap Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 49aaf57ff99c3e0af85cf0bd73290824 Package: Rsamtools Version: 2.20.0 Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6), R (>= 3.5.0) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 2.99.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: 3116aba15259d1cb8805248431de2d06 Package: rScudo Version: 1.20.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: ab019e3beb454a92af8ab34d3f96cbdc Package: rsemmed Version: 1.14.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: cb3a4912ccc0d0134d112906d2ab7f6a Package: RSeqAn Version: 1.24.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 46a0f5a43bdbc2f4f474d2a37f393630 Package: Rsubread Version: 2.18.0 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: b727beff13528e68b7bd6bcd51264ea6 Package: RSVSim Version: 1.44.0 Depends: R (>= 3.5.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign License: LGPL-3 MD5sum: 295ae63aa9964e418d4b08996955c8cf Package: rSWeeP Version: 1.16.0 Depends: R (>= 4.0) Imports: pracma, stats Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: cf6d8c6d7a1840c7e08b3acea1189ccb Package: RTCA Version: 1.56.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: 38574f322057f03762a7fcae8bbc2404 Package: RTCGA Version: 1.34.0 Depends: R (>= 3.3.0) Imports: XML, RCurl, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales, rmarkdown, htmltools Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr License: GPL-2 MD5sum: 923519c7139f9660637f882f8f1c48d8 Package: RTCGAToolbox Version: 2.34.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors (>= 0.23.10), stats, stringr, SummarizedExperiment, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 MD5sum: e99b83cc04de6c941a2b2d24fc9e3475 Package: RTN Version: 2.28.0 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 607940621bc8769b9b6c6d5befba5874 Package: RTNduals Version: 1.28.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 727b199227eafa3b0b830b0dfdd3050f Package: RTNsurvival Version: 1.28.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), RTNduals(>= 1.14.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 4b29e37e56259509c62eac7547f409fe Package: RTopper Version: 1.50.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: c4cc1f034fba72106c79747f4509073b Package: Rtpca Version: 1.14.0 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 MD5sum: 92ce306b093d96f5f7a1b475f81d6764 Package: rtracklayer Version: 1.64.0 Depends: R (>= 3.5.0), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, curl, httr, Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: 7611148b348d9330153379a8a0649900 Package: Rtreemix Version: 1.66.0 Depends: R (>= 2.5.0) Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL MD5sum: 8101709b749f6769ef44f3bdf57606a3 Package: rTRM Version: 1.42.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: methods, AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 8075b8bffcc7c9735528afd833301457 Package: rTRMui Version: 1.42.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: d2e03eab40a9bfd97c30c5b4859150ab Package: RUVcorr Version: 1.36.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db, rmarkdown License: GPL-2 MD5sum: 999660b1cc6e0e2644bf72b0469d3aac Package: RUVnormalize Version: 1.38.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: 0cf8da931c86828e1503910c5a4d154c Package: RUVSeq Version: 1.38.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: 3c33d2b1c14fcbb4599cbfa5381a5c4b Package: Rvisdiff Version: 1.2.0 Depends: R (>= 4.3.0) Imports: edgeR, utils Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager License: GPL-2 | GPL-3 MD5sum: 3f351158efc9eb7575e22d5a28be3186 Package: RVS Version: 1.26.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils, R.utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: 897bb47f2ffd544b147dd0dde3548702 Package: rWikiPathways Version: 1.24.0 Imports: httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr, readr, stringr, purrr, lubridate Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3986d578c92555f42030c3923d5fc862 Package: S4Arrays Version: 1.4.1 Depends: R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors, IRanges Imports: stats, crayon LinkingTo: S4Vectors Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 0a88d63245c0586e5ea13302df749337 Package: S4Vectors Version: 0.42.1 Depends: R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>= 0.37.0) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 771463710e0bde78b099b4f4636c7da2 Package: safe Version: 3.44.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: b48f94d1860126d0a78e96e58eac222f Package: sagenhaft Version: 1.74.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 9231522240bdf60cfb3434651d71df1e Package: SAIGEgds Version: 2.4.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.28.0), SeqArray (>= 1.42.3), Rcpp Imports: methods, stats, utils, Matrix, RcppParallel, CompQuadForm, survey LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, ggmanh, BiocGenerics License: GPL-3 MD5sum: 2542ec668fbcb20b54f9154dddba2f08 Package: sampleClassifier Version: 1.28.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: 232d5b6b066d0f7e2bc3df18491e22a0 Package: SamSPECTRAL Version: 1.58.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 0950e8255ce79915bf7989dc0576aa71 Package: sangeranalyseR Version: 1.14.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 MD5sum: bfb210444610e2dec73949bae5043a6e Package: sangerseqR Version: 1.40.0 Depends: R (>= 3.5.0), Biostrings, pwalign, stringr Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: aed6962d29d6439404b078b8330390f6 Package: SANTA Version: 2.40.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit License: GPL (>= 2) MD5sum: 5cc48ea68deedf4576a3ed934b16d77f Package: SARC Version: 1.2.0 Depends: R (>= 4.3), RaggedExperiment, GenomicRanges Imports: tidyverse, utils, reshape2, DescTools, metap, multtest, plyranges, data.table, scales, RColorBrewer, grid, gtable, gridExtra, GenomicFeatures, stats, ggplot2, plotly, IRanges Suggests: knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments License: GPL-3 MD5sum: cd0ed7670e9ea5fd21c880a14b912c90 Package: sarks Version: 1.16.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: db7f0958861526af6963ffb652aa88d8 Package: saseR Version: 1.0.0 Depends: R (>= 4.3.0) Imports: ASpli, S4Vectors, BiocGenerics, GenomicFeatures, MASS, PRROC, SummarizedExperiment, edgeR, pracma, precrec, BiocParallel, DESeq2, DEXSeq, data.table, limma, methods, GenomicRanges, GenomicAlignments, rrcov, MatrixGenerics, stats, IRanges, knitr, dplyr, igraph, parallel License: Artistic-2.0 MD5sum: c9ba1a05a267da21c898482e9002d1ee Package: satuRn Version: 1.12.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: 976eb461da93eb2f24e99c6fe126237e Package: SBGNview Version: 1.18.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: 933009f5304beeff199c3eda42159afc Package: SBMLR Version: 2.0.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: ebdf7460f912570f661496c1ba5f24c1 Package: SC3 Version: 1.32.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater, BiocStyle License: GPL-3 MD5sum: 67977946b991218ade2fa70d173faf30 Package: Scale4C Version: 1.26.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 9fdb15202aae04669c3989072c5a4185 Package: ScaledMatrix Version: 1.12.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats License: GPL-3 MD5sum: 8aded09aef46b6a15f3fec1b9ad929d8 Package: scanMiR Version: 1.10.0 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1f75f898bde05589fa1a3873a25f84d6 Package: scanMiRApp Version: 1.10.0 Depends: R (>= 4.0), scanMiR Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: 97726d5f52f572c83100200cd621586a Package: scAnnotatR Version: 1.10.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: 79055790b2768633f0e76ed6265614dd Package: SCAN.UPC Version: 2.46.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 959009229bdd623e029b7a569947542d Package: SCANVIS Version: 1.18.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: 2d3bd9ab94b5d1556eb95a7a23bfc517 Package: SCArray Version: 1.12.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.36.0), methods, DelayedArray (>= 0.28.0) Imports: S4Vectors, utils, Matrix, BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array License: GPL-3 MD5sum: ca5d61d8929a7a2a727670b8dab048ef Package: SCArray.sat Version: 1.4.0 Depends: methods, SCArray (>= 1.7.13), SeuratObject (>= 5.0), Seurat (>= 5.0) Imports: S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt, DelayedArray, BiocSingular, SummarizedExperiment, Matrix Suggests: future, RUnit, knitr, markdown, rmarkdown, BiocStyle License: GPL-3 MD5sum: d0a7fc39c8d5d441dff6e57fccab0fde Package: scatterHatch Version: 1.10.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 2ae44aa0403fdd52bad8e16c7a6dc294 Package: scBFA Version: 1.18.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: 95944d9e679c96490d207ccc23ce33e0 Package: SCBN Version: 1.22.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown,BiocStyle,BiocManager License: GPL-2 MD5sum: ef79576563b1360704c9cdcfe38f0c4b Package: scBubbletree Version: 1.6.0 Depends: R (>= 4.2.0) Imports: reshape2, future, future.apply, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: 862dc6e48ba156121a3946241ec42bbe Package: scCB2 Version: 1.14.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 6c859f1f091b9a4b69829999ec57a884 Package: scClassify Version: 1.16.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 3fe3c9925dc259c9412a6875e9e4cd5d Package: sccomp Version: 1.8.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1), rstan (>= 2.26.0), SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.26.0), StanHeaders (>= 2.26.0) Suggests: BiocStyle, testthat (>= 3.0.0), markdown, knitr, loo, tidyseurat, tidySingleCellExperiment, prettydoc Enhances: furrr, extraDistr License: GPL-3 MD5sum: 77b42ab7e799d0286fa8e340954496da Package: scDataviz Version: 1.14.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 3ba3f219bfcfec80039a77606700bf60 Package: scDblFinder Version: 1.18.0 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: 909f79351c16abdd076af8e34b05c7c7 Package: scDD Version: 1.28.0 Depends: R (>= 3.5.0) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: 3d2bb4e9b47f111cf70999f9a8a91182 Package: scDDboost Version: 1.6.0 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 7cba85865d0b1a188d107658bbe57758 Package: scde Version: 2.32.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: b5b2e577c559d25c0156b112713ce7da Package: scDesign3 Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: fc0c68f6469dd0f7b03c21129aef6980 Package: scds Version: 1.20.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: e6a77660053824fddc58276ce15687c1 Package: SCFA Version: 1.14.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: 638c77492c791c821a2d39cd225e59a5 Package: scFeatureFilter Version: 1.24.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: 5ac3470ddcb1bab56f68404fd7cfaf1a Package: scFeatures Version: 1.4.0 Depends: R (>= 4.2.0) Imports: DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler License: GPL-3 MD5sum: 980c2ddabd099a31be6532c0f9c05ed8 Package: scGPS Version: 1.18.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: 7406e6a97e7ec8dd7175576d21821387 Package: schex Version: 1.18.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 MD5sum: 5f4235202922b694f2898d2f1f7f9038 Package: scHOT Version: 1.16.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 485f148068fcefe77025c6b88a313376 Package: scider Version: 1.2.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, rlang, isoband, S4Vectors, grDevices Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: c5623658235f7d6e9701eb4d37860ad7 Package: scifer Version: 1.6.0 Imports: dplyr, rmarkdown, data.table, Biostrings, parallel, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods Suggests: fs, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a9de777746619181dcd4a26052e55954 Package: scmap Version: 1.26.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 7e15788334780cae17a03d0dc3a026e9 Package: scMerge Version: 1.20.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger License: GPL-3 MD5sum: d7bba4a5d26fb35d8fcaefb2c71d6a21 Package: scMET Version: 1.6.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: f43b227c2e351f4df8c2cb7ed6c7304d Package: scmeth Version: 1.24.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: b4e6d79b41b9b9dcbce91a753c312435 Package: scMitoMut Version: 1.0.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, zlibbioc, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: 6d06d68bb2bf51f4307ed6e20b526bda Package: scMultiSim Version: 1.0.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment Suggests: knitr, rmarkdown, roxygen2, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 8de00462822ad560ece00f0de1c14227 Package: SCnorm Version: 1.26.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: b5fa9be6bfba429ea2da6dac81fdc11e Package: scone Version: 1.28.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 2e26727cdf869d0455be76c07d02bc85 Package: Sconify Version: 1.24.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: d937f46b3d07c81c4dc9dc8ca7000610 Package: SCOPE Version: 1.16.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: 2941f068741ad801f26c8d1c54621a64 Package: scoreInvHap Version: 1.26.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 4f5bb4b94b14cbca529d00a2649b6cda Package: scPCA Version: 1.18.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 5742beea6e9e1658ccebf5c55814b5ce Package: scPipe Version: 2.4.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: c63a53eed2db45616f62429e7b9afd5a Package: scran Version: 1.32.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater License: GPL-3 MD5sum: 6049135bd63e4cbdf8776bdedc214e66 Package: scReClassify Version: 1.10.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE MD5sum: 0fc48adaf27efcbf684ec0dd940e9baf Package: scRecover Version: 1.20.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 460ccd3eefe632f24b9dc31686270380 Package: screenCounter Version: 1.4.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, zlibbioc, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: a01fb9b951659a11787d02ac05683321 Package: ScreenR Version: 1.6.0 Depends: R (>= 4.2) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>= 1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3), stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR (>= 3.32), tidyselect (>= 1.1.2) Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) License: MIT + file LICENSE MD5sum: 937a5bd66042ff44f588ecd1393ec9b6 Package: scRepertoire Version: 2.0.0 Depends: ggplot2, R (>= 4.0) Imports: cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, methods, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 4235040b17fdd41b48008d80c0e80e7d Package: scRNAseqApp Version: 1.4.0 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, data.table, DBI, DT, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle License: GPL-3 MD5sum: ba70b30f730f36f5d08921fc682d0314 Package: scruff Version: 1.22.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 2657322e022fb1116c79acd06dbabcf8 Package: scry Version: 1.16.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: 0bec393135901bbb239aba25f9b75392 Package: scShapes Version: 1.10.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 95a47ae21adcf2a0cbc0f5a84675c869 Package: scTensor Version: 2.14.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub License: Artistic-2.0 MD5sum: 9b6313bb9330f7bb64d44b9058bebfeb Package: scTGIF Version: 1.18.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: ef4d4bba5c75013b3a9342800b5c2459 Package: scTHI Version: 1.16.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 9d9b1dbf9076ce441d93e8f265939ee7 Package: scTreeViz Version: 1.10.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 MD5sum: 39763c220b10a9774af2a2e4a0ad27da Package: scuttle Version: 1.14.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran License: GPL-3 MD5sum: 85b39c35503190fe7a2d7c0e9f318e7c Package: scviR Version: 1.4.0 Depends: R (>= 4.3), basilisk, shiny, SingleCellExperiment Imports: reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater, stats, MatrixGenerics Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle License: Artistic-2.0 MD5sum: e684f66dbcc6aa7e8f7878fa0fbdc3bf Package: SDAMS Version: 1.24.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 0ca51b5c2b1dce4ae06f67aac1f281b1 Package: sechm Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, ComplexHeatmap Imports: S4Vectors, seriation, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: e296c2f2df3b1edfdb5d8c1db900b8aa Package: segmenter Version: 1.10.0 Depends: R (>= 4.1) Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: 1fbf454935faf751fabdc17c4085e3b4 Package: segmentSeq Version: 2.38.0 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 303d3841a69ec3c33410424d0b6ce573 Package: selectKSigs Version: 1.16.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 0aed9052fa803cbd1281a01634563bc3 Package: SELEX Version: 1.36.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: abf54c1113839e4a221ad900378e8425 Package: SemDist Version: 1.38.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 5787d0a685500edd0d05e8762c9f6b07 Package: semisup Version: 1.28.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: 58ecf4656786bd93b124f3af3544e4f4 Package: seq2pathway Version: 1.36.0 Depends: R (>= 3.6.2) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: 915e23850a11b8e359fc3945cd85b33d Package: seqArchR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods, stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2 (>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings, grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1) Suggests: cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0) License: GPL-3 | file LICENSE MD5sum: 08e5ab918adda4cbf7b878286ccb06e0 Package: seqArchRplus Version: 1.4.0 Depends: R (>= 4.2), GenomicRanges, IRanges, S4Vectors Imports: BiocParallel, Biostrings, BSgenome, ChIPseeker, cli, clusterProfiler, cowplot, factoextra, GenomeInfoDb, ggplot2, ggimage, graphics, grDevices, gridExtra, heatmaps, magick, methods, RColorBrewer, scales, seqArchR, seqPattern, stats, utils Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun License: GPL-3 MD5sum: 49fa131a5cb5845731b9517ac394af0e Package: SeqArray Version: 1.44.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: 85db6a4694833397e8369df196a50a60 Package: seqCAT Version: 1.26.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: 19ed58281b95d3a00a031e13dcf806be Package: seqcombo Version: 1.26.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: e1899a350cd970bda0f6f3aa8f48eb14 Package: SeqGate Version: 1.14.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 73730b0413d3818c0f0313daf352d8ca Package: SeqGSEA Version: 1.44.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) MD5sum: 4931e1fe3d03e02e234c2c21e9a97869 Package: seq.hotSPOT Version: 1.4.0 Depends: R (>= 3.5.0) Imports: R.utils, hash, stats, base, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: ee56c26dbbb9a42c4233aef525d62dff Package: seqLogo Version: 1.70.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: e8fa6474c75dce96a800bd8ea1cd634d Package: seqPattern Version: 1.36.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 27384330a92182a3aff9b53a9221f7ba Package: seqsetvis Version: 1.24.0 Depends: R (>= 3.6), ggplot2 Imports: cowplot, data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 42e80a5cfad3e1d1f4b3d0305b6fdd03 Package: SeqSQC Version: 1.26.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 43cdff4c69777102813765931d79e80c Package: seqTools Version: 1.38.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: b805de59e252042752686219ba7c9605 Package: SeqVarTools Version: 1.42.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 MD5sum: f487ec7e897942a4932b110a9b736505 Package: sesame Version: 1.22.2 Depends: R (>= 4.3.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2 Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: ef2f48ab33f70bc7534d411b92d273c7 Package: SEtools Version: 1.18.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: 8d120a38828324e9856cd92ea53598e2 Package: sevenbridges Version: 1.34.0 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: e6ed26a13693bba7efb32fd0a2b44a43 Package: sevenC Version: 1.24.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 MD5sum: bcb42f0f9d0f9fe0fac05c061630301c Package: SGSeq Version: 1.38.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: 6e8491ef20577a645c5edc9bd8d4197b Package: SharedObject Version: 1.18.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: a3ff7ccc8ed8d77d9f112832e42d3e63 Package: shinyepico Version: 1.12.0 Depends: R (>= 4.3.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle License: AGPL-3 + file LICENSE MD5sum: 09f5b9feab395ee9d44f567b6f6f0cf1 Package: shiny.gosling Version: 1.0.0 Imports: htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 MD5sum: 538d9ede6938c6b01d274abf818c7ea0 Package: shinyMethyl Version: 1.40.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 7d52a20555f4fe3d58fe26daa3451dd8 Package: ShortRead Version: 1.62.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, zlibbioc, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: 733128a3ee9524d5547903a6126bdac5 Package: SIAMCAT Version: 2.8.0 Depends: R (>= 4.2.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: 40fd7942220c7015459c74d8f1a2f2a4 Package: SICtools Version: 1.34.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 60fc0d75c3e581d920c167b4c612d057 Package: SigCheck Version: 2.36.0 Depends: R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: 4304af149dbd896f61f2654b17fe29c6 Package: sigFeature Version: 1.22.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL (>= 2) MD5sum: 5428fce7e1f653506866072e47410bec Package: SigFuge Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: 01a13939cb8df15542b4c9d2efa2613f Package: siggenes Version: 1.78.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 93b8085ccabb50984c67295f7c9c460c Package: sights Version: 1.30.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 1c3adc0842a6a1adda82a1bf5428bd41 Package: signatureSearch Version: 1.18.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: f2765546aaba7ead766507346e330070 Package: signeR Version: 2.6.0 Depends: R (>= 3.0.2), VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: e81baf2eba686859ee5940c4c3017606 Package: signifinder Version: 1.6.0 Depends: R (>= 4.3.0) Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, sparrow, SpatialExperiment, stats, SummarizedExperiment, survival, survminer, viridis Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 94b4256dbd5cb9030ae0b2d199f4c491 Package: SigsPack Version: 1.18.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 0082640a4b57bb67570e08f6d18b98a1 Package: sigsquared Version: 1.36.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 5c6838317235e77a2d2ab1c0db2dcbc0 Package: SIM Version: 1.74.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: 968f14d18716424e370f7d235278682d Package: SIMAT Version: 1.36.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 083d599318a78647990075e61b35a081 Package: SimBu Version: 1.6.0 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: d5df307414239d5499a2d11de668964f Package: SIMD Version: 1.22.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: 76b90d22791c580744d5b952d31d65ed Package: SimFFPE Version: 1.16.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 360fbc1ab652ced4f44d248a4f484bbf Package: similaRpeak Version: 1.36.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 0e1dcbb2214507f15581d0d93da2a17f Package: SIMLR Version: 1.30.0 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: 3f2c8ae9603c107e9e5cf382e403148a Package: simona Version: 1.2.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: e9021b4110297cd9b73ffad458640f88 Package: simPIC Version: 1.0.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, Matrix, stats, SummarizedExperiment, actuar, rlang, S4Vectors, methods, scales, scuttle Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 25836f785bc464dfdc0d6af181f0fa2e Package: simpleSeg Version: 1.6.1 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: 2ba72aa59205b7ca1e7b071ec0fc8c80 Package: simplifyEnrichment Version: 1.14.0 Depends: R (>= 3.6.0), BiocGenerics, grid Imports: GOSemSim, ComplexHeatmap (>= 2.7.4), circlize, GetoptLong, digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: 263470bad039479f9cb746fb4f87ff36 Package: sincell Version: 1.36.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: e06df075a06a8ccdad041673399df28d Package: single Version: 1.8.0 Depends: R (>= 4.0) Imports: Biostrings, BiocGenerics, dplyr, GenomicAlignments,IRanges, methods, reshape2, rlang, Rsamtools, stats, stringr, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8394a9922ecb70bc9af181e24ccee423 Package: SingleCellAlleleExperiment Version: 1.0.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7a4c45af3ef2344a6f00d5871c89dbed Package: SingleCellExperiment Version: 1.26.0 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: b9770a9b79614f3f442f9ec7180f01d7 Package: SingleCellSignalR Version: 1.16.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 7b9a42d612709a47f6019e4d0dd870f4 Package: singleCellTK Version: 2.14.0 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, anndata, AnnotationHub, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, eds, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats, zellkonverter Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE MD5sum: 78ef577ffbc162827515148501d8abba Package: SingleMoleculeFootprinting Version: 1.12.0 Depends: R (>= 4.1.0) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, data.table, grDevices, plyr, IRanges, RColorBrewer, stats, QuasR Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 595e27ae6a307c98180016dcf6962a8f Package: SingleR Version: 2.6.0 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel LinkingTo: Rcpp, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 + file LICENSE MD5sum: 4dd535d1e58940e651075e00b7a03c63 Package: singscore Version: 1.24.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: bda3182af1c7a4677457398ef4005279 Package: SiPSiC Version: 1.4.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE MD5sum: bde74ea557eef8cafb95837bcc9ac686 Package: sitadela Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker, utils Suggests: BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: 6ded1dc608cf75a6cf586e02b057f222 Package: sitePath Version: 1.20.0 Depends: R (>= 4.1) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 66ac865b5346fb59f13e4fccce328691 Package: sizepower Version: 1.74.0 Depends: stats License: LGPL MD5sum: a54ecde1035371f45b7c25086e6ed4f6 Package: sketchR Version: 1.0.0 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment License: MIT + file LICENSE MD5sum: 3960806851615cd4494456cac76c89a4 Package: skewr Version: 1.36.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: cf8605997cb53e6c78b51c27d93c8c7a Package: slingshot Version: 2.12.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: bf15af0eca81c14e07136d9eb4cd8847 Package: SLqPCR Version: 1.70.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: f3e9a535c074222d03928230e26df99f Package: SMAD Version: 1.20.0 Depends: R (>= 3.6.0), RcppAlgos Imports: magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: c5089e276ab32ab77a032804cd502187 Package: SMAP Version: 1.68.0 Depends: R (>= 2.10), methods License: GPL-2 MD5sum: d3a45bff410a78ddd8ccd3c0f32b6e0b Package: smartid Version: 1.0.2 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE MD5sum: 4e95b2e33f9eaabad0394c22df742389 Package: SMITE Version: 1.32.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 1d17087cad6cdd183dd0d97413112ef2 Package: smoothclust Version: 1.0.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, sparseMatrixStats, spdep, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: 6f310a1daf3f3bd3b6f2f82492abe847 Package: SNAGEE Version: 1.44.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: 3dcc8cc874a49c713119ce482ff8524e Package: snapcount Version: 1.16.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: f378e77d4702e65615e61848d7ccbe2b Package: snifter Version: 1.14.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: eda790ff3196a1da5b366169f93b8ade Package: snm Version: 1.52.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: d01ab36fa82b39c60a8f457c6654662a Package: SNPediaR Version: 1.30.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 6a872e7fe1dd8636c8ad44318d7ddc19 Package: SNPhood Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb (>= 1.34.8), BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) MD5sum: fbba570621fec0d80aaa3e264ab5e39b Package: SNPRelate Version: 1.38.0 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: 5bd6f652f26293214134ffb797650377 Package: snpStats Version: 1.54.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 MD5sum: dda9559fe3b77978ed36c0dcbbd53c40 Package: soGGi Version: 1.36.0 Depends: R (>= 3.5.0), BiocGenerics, SummarizedExperiment Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel Suggests: testthat, BiocStyle, knitr License: GPL (>= 3) MD5sum: 789aa1074ebf24f8a213ccdd7ccfc988 Package: SOMNiBUS Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr, yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr, Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: 57cadc8c5184467b7137ab6ac6ebf13c Package: SpaceMarkers Version: 1.0.0 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, jsonlite, Matrix, qvalue, stats, utils, methods Suggests: data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS License: MIT + file LICENSE MD5sum: e92c819c8c47bb085a1c768e2f7299e6 Package: SpacePAC Version: 1.42.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: c62e3c3c983d3a5bc6c26410408c6c1f Package: Spaniel Version: 1.18.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE MD5sum: e153ee0220e85a43fd2ca5c921234bf9 Package: sparrow Version: 1.10.1 Depends: R (>= 4.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: 1bf5fdd63e0a624b7e120bdea97f8fb5 Package: SparseArray Version: 1.4.8 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors, S4Arrays (>= 1.4.1) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: DelayedArray, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 6a5eec6f9d34b656a3a344bf2c6dd3fa Package: sparseDOSSA Version: 1.28.0 Imports: stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack Suggests: knitr, BiocStyle, BiocGenerics, rmarkdown License: MIT + file LICENSE MD5sum: a4f5b04552c19360f057e18b7f31a63c Package: sparseMatrixStats Version: 1.16.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 76fc6fd3706fbe7c67d127df3168629a Package: sparsenetgls Version: 1.22.0 Depends: R (>= 4.0.0), Matrix, MASS Imports: methods, glmnet, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: 56b1714d0b3cdc53ff46450ce41da706 Package: SparseSignatures Version: 2.14.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2 Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: 09dbad560988d913d5490fa19a885c8b Package: spaSim Version: 1.6.0 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 MD5sum: d18c2a958bd41ef45ffdadf9f4d80c49 Package: SpatialCPie Version: 1.20.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE MD5sum: b439364eda79252d3348013f218de1b8 Package: spatialDE Version: 1.10.0 Depends: R (>= 4.3) Imports: reticulate, basilisk (>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, ggplot2, ggrepel, scales, gridExtra Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 23d4895da432f7e7879676ccf3cb8550 Package: SpatialDecon Version: 1.14.0 Depends: R (>= 4.0.0) Imports: grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE MD5sum: 4d408328a360536ca1f4cf62d09e996b Package: SpatialExperiment Version: 1.14.0 Depends: methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils License: GPL-3 MD5sum: b48de62f39fc6348ffd6f3743d2dbb74 Package: spatialHeatmap Version: 2.10.1 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, gplots, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, scater, scuttle, scran, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: 52302c08172f8702562b2c2504c88a37 Package: SpatialOmicsOverlay Version: 1.4.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: fed6ae72215201240235d7537d8aed29 Package: speckle Version: 1.4.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: cfdd6505c3c605c730ff7e1ff77b8901 Package: specL Version: 1.38.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: 472f6123fcc13f2d97f92a584941e85e Package: SpeCond Version: 1.58.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: c65d69f2358bebe3bb8910311b4774dc Package: Spectra Version: 1.14.1 Depends: R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics (>= 1.35.4) Imports: methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick License: Artistic-2.0 MD5sum: 27a92f2e544f1696b5dfaddabe1c5b15 Package: SpectralTAD Version: 1.20.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE MD5sum: 480862ecfdb20ddb64f338919f6e8ea9 Package: SPEM Version: 1.44.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: 20911841ac3bbedaaa18d17a68e84edf Package: SPIA Version: 2.56.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes MD5sum: f2b614b9fed5e14774f688d3e92e475a Package: SPIAT Version: 1.6.1 Depends: R (>= 4.2.0), SpatialExperiment (>= 1.8.0) Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp, SummarizedExperiment, rlang Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa License: Artistic-2.0 + file LICENSE MD5sum: 98cd54a2e35a69c64c2fe3b3453b5f9b Package: spicyR Version: 1.16.1 Depends: R (>= 4.1) Imports: ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli Suggests: BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 6312cb836653e203a84d83ee970121e4 Package: spikeLI Version: 2.64.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: ec2acf20d351923ae37ae488f32b2b2b Package: spiky Version: 1.10.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 MD5sum: 71914fea71bbeaf2c723a547c05903fa Package: spillR Version: 1.0.0 Depends: R (>= 4.3.0), SummarizedExperiment, CATALYST Imports: dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.geom, S4Vectors, parallel Suggests: knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin License: LGPL-3 MD5sum: 08dc4c378564c53e2ab20e2f34d8d2c6 Package: spkTools Version: 1.60.0 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) MD5sum: 835c340d4b0f408d5ffcd8444815d333 Package: splatter Version: 1.28.0 Depends: R (>= 4.0), SingleCellExperiment Imports: BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods, rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils, withr Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), IRanges, igraph, knitr, limSolve, lme4, magick, mfa, phenopath, progress, preprocessCore, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave, License: GPL-3 + file LICENSE MD5sum: d3857b573c1510d37d4354643daf0822 Package: SpliceWiz Version: 1.6.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: ompBAM, methods, stats, utils, tools, parallel, scales, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest LinkingTo: ompBAM, Rcpp, zlibbioc, RcppProgress Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread License: MIT + file LICENSE MD5sum: 116dd084de2db7216aa0f59054bfb4f4 Package: SplicingFactory Version: 1.12.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE MD5sum: 395d5327c4486572329b0609a0180a57 Package: SplicingGraphs Version: 1.44.0 Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb, GenomicRanges (>= 1.23.21), Rsamtools, graph Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: 510df14f4085ddb65d0098f214882a86 Package: splineTimeR Version: 1.32.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 MD5sum: 37fe546f9a1085d7d22dc471b76dfcaa Package: splots Version: 1.70.0 Imports: grid, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 License: LGPL MD5sum: 194e03bc91ff91696873c4dfd0e6e7b5 Package: SPONGE Version: 1.26.0 Depends: R (>= 3.6) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, miRBaseConverter, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA License: GPL (>= 3) MD5sum: cf70375a0774ec1fee253510ff549db1 Package: spoon Version: 1.0.0 Depends: R (>= 4.4) Imports: SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix, methods, SummarizedExperiment, stats, utils, scuttle Suggests: testthat, STexampleData, knitr License: MIT + file LICENSE MD5sum: e4dc6d8c1bdc34307b330df89a1be326 Package: SpotClean Version: 1.6.1 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: 37673f3594f49a428dbc3affb0ca5a34 Package: SPOTlight Version: 1.8.0 Depends: R (>= 4.1) Imports: ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, sparseMatrixStats, stats Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 MD5sum: 8b302d11f4c383bfd8ca2deaef8fe3ce Package: SpotSweeper Version: 1.0.0 Depends: R (>= 4.3.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: db9204e3151280b1e505c7deedbc3ac8 Package: spqn Version: 1.16.0 Depends: R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics Imports: graphics, stats, utils, matrixStats Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit License: Artistic-2.0 MD5sum: f89f5ecbe7e6a4c618bb8efb01f9a538 Package: SPsimSeq Version: 1.14.0 Depends: R (>= 4.0) Imports: stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle License: GPL-2 MD5sum: 0baaf0074149eeff3b542a48beb1705a Package: SQLDataFrame Version: 1.18.0 Depends: DelayedArray, S4Vectors Imports: stats, utils, methods, BiocGenerics, RSQLite, duckdb, DBI Suggests: knitr, rmarkdown, BiocStyle, testthat MD5sum: 3826253c9f1126892a6fbc6a352554a6 Package: SQUADD Version: 1.54.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>= 2) MD5sum: 3961357b3a71be9e12c2ace572f250f2 Package: sRACIPE Version: 1.20.0 Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture License: MIT + file LICENSE MD5sum: c142094b8d9a297dc13d49afcdca7c79 Package: SRAdb Version: 1.66.0 Depends: RSQLite, graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 MD5sum: 24c547173a75a007add9d297a2c15b0b Package: srnadiff Version: 1.24.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), stats, methods, devtools, S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, edgeR, Rsamtools, GenomicFeatures, GenomicAlignments, grDevices, Gviz, BiocParallel, BiocManager, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocManager, BiocStyle License: GPL-3 MD5sum: fae25b2e7b65370dfbb5336e544bc961 Package: sscu Version: 2.34.0 Depends: R (>= 3.3) Imports: Biostrings (>= 2.36.4), seqinr (>= 3.1-3), BiocGenerics (>= 0.16.1) Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: d1146fc94fdd3a387e44904e3a2ce6e3 Package: sSeq Version: 1.42.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) MD5sum: f60a6327bd19945edbdf27800d9e4d32 Package: ssize Version: 1.78.0 Depends: gdata, xtable License: LGPL MD5sum: 89e14934cfb4006f2a090e391ed0f7e8 Package: sSNAPPY Version: 1.8.0 Depends: R (>= 4.3.0), ggplot2 Imports: dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble, ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, pheatmap, utils, stringr, gtools, tidyr Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 8b894d22a3da78b8722b0e439c05ddc5 Package: ssPATHS Version: 1.18.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: ROCR, dml, MESS Suggests: ggplot2, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 5c57c53b8906cac5cc265843ee4ba6b7 Package: ssrch Version: 1.20.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 132a52d0d868ed71f4d11d3c1630c10b Package: ssviz Version: 1.38.0 Depends: R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape, ggplot2, RColorBrewer, stats Suggests: knitr License: GPL-2 MD5sum: 83775bdbcddfd9c5f53ce1cdf3e614fc Package: stageR Version: 1.26.0 Depends: R (>= 3.4), SummarizedExperiment Imports: methods, stats Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat License: GNU General Public License version 3 MD5sum: 3ebfd238a45ad0bd9436edc964ba7e0a Package: standR Version: 1.8.0 Depends: R (>= 4.1) Imports: dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment, SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2, tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics, grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 30b3197fa1ce6d83e9153315d457868b Package: staRank Version: 1.46.0 Depends: methods, cellHTS2, R (>= 2.10) License: GPL MD5sum: 7754eecd72e7c8b6a33138f12e3948d6 Package: STATegRa Version: 1.40.0 Depends: R (>= 2.10) Imports: Biobase, gridExtra, ggplot2, methods, stats, grid, MASS, calibrate, gplots, edgeR, limma, foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 MD5sum: b8714cf1ad954c2e02f8eccead4ac56e Package: Statial Version: 1.6.0 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: GPL-3 MD5sum: dd2e63aa5f70fb5feb41ef88c8f82d10 Package: statTarget Version: 1.34.0 Depends: R (>= 3.6.0) Imports: randomForest,plyr,pdist,ROC,utils,grDevices,graphics,rrcov,stats, pls,impute Suggests: testthat, BiocStyle, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 2b43e4ea6bac8dac86a151b9d150af38 Package: STdeconvolve Version: 1.8.0 Depends: R (>= 4.1) Imports: topicmodels, BiocParallel, Matrix, methods, mgcv, ggplot2, scatterpie, viridis, slam, stats, clue, liger, reshape2, graphics, grDevices, utils Suggests: knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel License: GPL-3 MD5sum: 4c78fe49511847757d09425c3e6d4e8a Package: stepNorm Version: 1.76.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL MD5sum: 4608c851f67d430b57d8e1974e24b9ca Package: stJoincount Version: 1.6.0 Depends: R (>= 4.2.0) Imports: graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: e925e671a5bdab2c6b3d51e2f5460e87 Package: strandCheckR Version: 1.22.0 Imports: dplyr, magrittr, GenomeInfoDb, GenomicAlignments, GenomicRanges, IRanges, Rsamtools, S4Vectors, grid, BiocGenerics, ggplot2, reshape2, stats, gridExtra, TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr, rmarkdown Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: c470b09e445bb780704ed185597f22e6 Package: Streamer Version: 1.50.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 MD5sum: 93a3798b0cdb60c4c3349fae2b045ca1 Package: STRINGdb Version: 2.16.4 Depends: R (>= 2.14.0) Imports: png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots, hash, plotrix Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: d8964901e56085cf353a799cfbfe9d17 Package: STROMA4 Version: 1.28.0 Depends: R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats, stats, graphics, utils Suggests: breastCancerMAINZ License: GPL-3 MD5sum: 716961f800faca5483415dc52f1b2fa3 Package: struct Version: 1.16.0 Depends: R (>= 4.0) Imports: methods,ontologyIndex, datasets, graphics, stats, utils, knitr, SummarizedExperiment, S4Vectors, rols Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick License: GPL-3 MD5sum: 88df773b7d4af6a8ded8dfabe296186d Package: Structstrings Version: 1.20.0 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), Biostrings (>= 2.57.2) Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 MD5sum: 3334f6344a945fa58e6551130f21b3e7 Package: structToolbox Version: 1.16.0 Depends: R (>= 4.0), struct (>= 1.5.1) Imports: ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs License: GPL-3 MD5sum: 1feeff63be07579098791e0dda021462 Package: StructuralVariantAnnotation Version: 1.20.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0) Imports: assertthat, Biostrings, pwalign, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb, Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, License: GPL-3 + file LICENSE MD5sum: 97071665ed755fcf25bf03be07b5c6b1 Package: SubCellBarCode Version: 1.20.0 Depends: R (>= 3.6) Imports: Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats, org.Hs.eg.db, AnnotationDbi Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: ea4b92f3c47a52dbf2fb8f5b07eff69f Package: subSeq Version: 1.34.0 Depends: R (>= 3.2) Imports: data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99), digest, Biobase Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr License: MIT + file LICENSE MD5sum: aba319b28ca5cc7e6a78233f0b06cb4e Package: SUITOR Version: 1.6.0 Depends: R (>= 4.2.0) Imports: stats, utils, graphics, ggplot2, BiocParallel Suggests: devtools, MutationalPatterns, RUnit, BiocManager, BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 3b207cb6886266fe96f751f0984d622e Package: SummarizedExperiment Version: 1.34.0 Depends: R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3), GenomicRanges (>= 1.55.2), Biobase Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), S4Arrays (>= 1.1.1), DelayedArray (>= 0.27.1) Suggests: HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite, rhdf5, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest License: Artistic-2.0 MD5sum: 08dbcb9ec119b2dc0c171eb5eb4c2c2c Package: Summix Version: 2.10.0 Depends: R (>= 4.3) Imports: dplyr, nloptr, magrittr, methods, tibble, tidyselect, BEDASSLE, scales, visNetwork, randomcoloR Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 03f86a4c3c53357970e571e54191ee5e Package: supersigs Version: 1.12.0 Depends: R (>= 4.1) Imports: assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation License: GPL-3 MD5sum: 2ad3ceaf24624e693236efb8972984af Package: supraHex Version: 1.42.0 Depends: R (>= 3.6), hexbin Imports: ape, MASS, grDevices, graphics, stats, readr, tibble, tidyr, dplyr, stringr, purrr, magrittr, igraph, methods License: GPL-2 MD5sum: 287e82c7717bb8e4cfae301eaf09cc52 Package: surfaltr Version: 1.10.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0.6), biomaRt (>= 2.46.0), protr (>= 1.6-2), seqinr (>= 4.2-5), ggplot2 (>= 3.3.2), utils (>= 2.10.1), stringr (>= 1.4.0), Biostrings (>= 2.58.0),readr (>= 1.4.0), httr (>= 1.4.2), testthat(>= 3.0.0), xml2(>= 1.3.2), msa (>= 1.22.0), methods (>= 4.0.3) Suggests: knitr, rmarkdown, devtools, kableExtra License: MIT + file LICENSE MD5sum: 7413533b6169ff33bbdcd5388de823ae Package: SurfR Version: 1.0.0 Depends: R (>= 4.3.0) Imports: httr, BiocFileCache, BiocStyle, SPsimSeq, DESeq2, edgeR, openxlsx, stringr, rhdf5, ggplot2, ggrepel, stats, magrittr, assertr, tidyr, dplyr, TCGAbiolinks, biomaRt, metaRNASeq, enrichR, scales, venn, gridExtra, SummarizedExperiment, knitr, grDevices, graphics, utils Suggests: testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: b209cf9de9b9f0b8dba6794e0c82ac43 Package: survcomp Version: 1.54.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: 42b6c83222b73cacfce918c26d77d945 Package: survtype Version: 1.20.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2aa17d0e134c0a792f477097f906b3a3 Package: sva Version: 3.52.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: 60f21682b167fda7ff9a65862c67e667 Package: svaNUMT Version: 1.10.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0) Imports: assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures, pwalign Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 2145e77bc2d38d3cd0f92a0e9fae41ee Package: svaRetro Version: 1.10.0 Depends: GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0) Imports: VariantAnnotation, assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomicFeatures, GenomeInfoDb, S4Vectors, utils Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: c9ff002268b00dcd363d204c93199290 Package: SVMDO Version: 1.4.0 Depends: R(>= 4.3), shiny (>= 1.7.4) Imports: shinyFiles (>= 0.9.3), shinytitle (>= 0.1.0), golem (>= 0.3.5), nortest (>= 1.0-4), e1071 (>= 1.7-12), BSDA (>= 1.2.1), data.table (>= 1.14.6), sjmisc (>= 2.8.9), klaR (>= 1.7-1), caTools (>= 1.18.2), caret (>= 6.0-93), survival (>= 3.4-0), DOSE (>= 3.24.2), AnnotationDbi (>= 1.60.0), org.Hs.eg.db (>= 3.16.0), dplyr (>= 1.0.10), SummarizedExperiment (>= 1.28.0), grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6) License: GPL-3 MD5sum: a530ce7abc22259331c6853883d5b25d Package: SwathXtend Version: 2.26.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 MD5sum: e06a089d656fb4527fea689e4828ba9e Package: swfdr Version: 1.30.0 Depends: R (>= 3.4) Imports: methods, splines, stats4, stats Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat License: GPL (>= 3) MD5sum: 8dcc325db0dd8822f4bf20f11c962d7c Package: switchBox Version: 1.40.0 Depends: R (>= 2.13.1), pROC, gplots License: GPL-2 MD5sum: fc3cb895473fcc5c2655f923db16a315 Package: switchde Version: 1.30.0 Depends: R (>= 3.4), SingleCellExperiment Imports: SummarizedExperiment, dplyr, ggplot2, methods, stats Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr License: GPL (>= 2) MD5sum: 02ec9d472809262e80ee8b92dcd96e0d Package: synapsis Version: 1.10.0 Depends: R (>= 4.1) Imports: EBImage, stats, utils, graphics Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle License: MIT + file LICENSE MD5sum: cbb1fb4613556de7d3be98081110686c Package: synapter Version: 2.28.0 Depends: R (>= 3.1.0), methods, MSnbase (>= 2.1.2) Imports: RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0) Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr License: GPL-2 MD5sum: ba050c2501a35f12317f95ec5d7092ad Package: synergyfinder Version: 3.12.0 Depends: R (>= 4.0.0) Imports: drc (>= 3.0-1), reshape2 (>= 1.4.4), tidyverse (>= 1.3.0), dplyr (>= 1.0.3), tidyr (>= 1.1.2), purrr (>= 0.3.4), furrr (>= 0.2.2), ggplot2 (>= 3.3.3), ggforce (>= 0.3.2), grid (>= 4.0.2), vegan (>= 2.5-7), gstat (>= 2.0-6), sp (>= 1.4-5), methods (>= 4.0.2), SpatialExtremes (>= 2.0-9), ggrepel (>= 0.9.1), kriging (>= 1.1), plotly (>= 4.9.3), stringr (>= 1.4.0), future (>= 1.21.0), mice (>= 3.13.0), lattice (>= 0.20-41), nleqslv (>= 3.3.2), stats (>= 4.0.2), graphics (>= 4.0.2), grDevices (>= 4.0.2), magrittr (>= 2.0.1), pbapply (>= 1.4-3), metR (>= 0.9.1) Suggests: knitr, rmarkdown License: Mozilla Public License 2.0 MD5sum: 32da8be8b7091518d677b90c76ac71ff Package: SynExtend Version: 1.16.0 Depends: R (>= 4.3.0), DECIPHER (>= 2.28.0) Imports: methods, Biostrings, S4Vectors, IRanges, utils, stats, parallel, graphics, grDevices, RSQLite, DBI Suggests: BiocStyle, knitr, igraph, markdown, rmarkdown License: GPL-3 MD5sum: eca123c7c62522861b7ed8a4a0559c53 Package: synlet Version: 2.4.0 Depends: R (>= 3.5.0) Imports: data.table, ggplot2, grDevices, magrittr, methods, patchwork, RankProd, RColorBrewer, stats, utils Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 MD5sum: a28c8c4bec7708b3386d7246d9e5782f Package: SynMut Version: 1.20.0 Imports: seqinr, methods, Biostrings, stringr, BiocGenerics Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue License: GPL-2 MD5sum: 261e26a5a3dffd3033f7ccb3f35126f8 Package: syntenet Version: 1.6.0 Depends: R (>= 4.2) Imports: Rcpp (>= 1.0.8), BiocParallel, GenomicRanges, rlang, Biostrings, rtracklayer, utils, methods, igraph, stats, grDevices, RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph, networkD3 LinkingTo: Rcpp, testthat Suggests: BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2 License: GPL-3 MD5sum: d5bf309f35304c7813c710e5e75a6aa7 Package: systemPipeR Version: 2.10.0 Depends: Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1), methods Imports: GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr, magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures, txdbmaker, VariantAnnotation (>= 1.25.11) License: Artistic-2.0 MD5sum: 6ffb6f48618e10ab0dd1b8237ce415f7 Package: systemPipeShiny Version: 1.14.0 Depends: R (>= 4.0.0), shiny (>= 1.6.0), spsUtil (>= 0.2.2), spsComps (>= 0.3.3), drawer (>= 0.2) Imports: DT, assertthat, bsplus, crayon, dplyr, ggplot2, htmltools, glue, magrittr, methods, plotly, rlang, rstudioapi, shinyAce, shinyFiles, shinyWidgets, shinydashboard, shinydashboardPlus (>= 2.0.0), shinyjqui, shinyjs, shinytoastr, stringr, stats, styler, tibble, utils, vroom (>= 1.3.1), yaml, R6, RSQLite, openssl Suggests: testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>= 2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr, pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.1.0), cicerone License: GPL (>= 3) MD5sum: 43e6a6b024fc055a0b80c43e3a04abde Package: systemPipeTools Version: 1.12.0 Imports: DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr, ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble, magrittr, DT, stats Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods License: Artistic-2.0 MD5sum: ca0948a238630ed14daee3b19b4a307e Package: tadar Version: 1.2.1 Depends: GenomicRanges, ggplot2, R (>= 4.3.0) Imports: BiocGenerics, GenomeInfoDb, Gviz, IRanges, MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats, VariantAnnotation Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: a7ad55623a295e470ec97015d41cabba Package: TADCompare Version: 1.14.0 Depends: R (>= 4.0) Imports: dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, SpectralTAD, magick, qpdf License: MIT + file LICENSE MD5sum: e5af6ce142997881b5ccb500e47fb21b Package: tanggle Version: 1.10.0 Depends: R (>= 4.1), ggplot2 (>= 2.2.0), ggtree Imports: ape (>= 5.0), phangorn (>= 2.5), utils, methods Suggests: tinytest, BiocStyle, ggimage, knitr, rmarkdown License: Artistic-2.0 MD5sum: 254aa35e3649d42203ed61fddc7667a9 Package: TAPseq Version: 1.16.0 Depends: R (>= 4.0.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle License: MIT + file LICENSE MD5sum: bc76d227cca4e4b21e09303df5dd24dd Package: target Version: 1.18.0 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 MD5sum: 7efc1adfd623a11f2866bd58f58ca1ad Package: TargetDecoy Version: 1.10.0 Depends: R (>= 4.1) Imports: ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr License: Artistic-2.0 MD5sum: 661ca47dbf8c8cadbb113aa0aed630d3 Package: TargetScore Version: 1.42.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: 5b1c6b5053b03dba561723ec6648f642 Package: TargetSearch Version: 2.6.2 Imports: graphics, grDevices, methods, ncdf4, stats, utils, assertthat Suggests: TargetSearchData, BiocStyle, knitr, tinytest License: GPL (>= 2) MD5sum: 597ebc966c41eef623190db1fccebec2 Package: TBSignatureProfiler Version: 1.16.0 Depends: R (>= 4.2.0) Imports: ASSIGN (>= 1.23.1), BiocParallel, ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA (>= 1.51.3), magrittr, methods, RColorBrewer, reshape2, rlang, ROCit, S4Vectors, singscore, stats, SummarizedExperiment Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat License: MIT + file LICENSE MD5sum: c9388fe0eb609f0539dd8ccc9794d749 Package: TCC Version: 1.44.0 Depends: R (>= 3.0), methods, DESeq2, edgeR, ROC Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 050c85683d32bcd83c0855bc84f1dc44 Package: TCGAutils Version: 1.24.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 3e891261821083f0a815732f0bb69684 Package: TCseq Version: 1.28.0 Depends: R (>= 3.4) Imports: edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges, SummarizedExperiment, GenomicAlignments, Rsamtools, e1071, cluster, ggplot2, grid, grDevices, stats, utils, methods, locfit Suggests: testthat License: GPL (>= 2) MD5sum: d53e7c76486ba5877d8d462cff1ac14d Package: TDbasedUFE Version: 1.4.0 Imports: GenomicRanges, rTensor, readr, methods, MOFAdata, tximport, tximportData, graphics, stats, utils, shiny Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: c7fdc96d1ffd8f44f8cd75117e2ead8b Package: TDbasedUFEadv Version: 1.4.0 Imports: TDbasedUFE, Biobase, GenomicRanges, utils, rTensor, methods, graphics, RTCGA, stats, enrichplot, DOSE, STRINGdb, enrichR, hash, shiny Suggests: knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq, RTCGA.clinical, BiocStyle, MOFAdata License: GPL-3 MD5sum: 53815047193677404e47c8030ebfe905 Package: TEKRABber Version: 1.8.0 Depends: R (>= 4.3) Imports: apeglm, biomaRt, dplyr, doParallel, DESeq2, foreach, GenomeInfoDb, magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny, knitr, testthat (>= 3.0.0) License: LGPL (>= 3) MD5sum: 998f10735caffb6ed096dbfe880bf458 Package: TEQC Version: 4.26.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: 41a8a57e1e1025228aeb1bfc18b1d662 Package: ternarynet Version: 1.48.0 Depends: R (>= 4.0) Imports: utils, igraph, methods, graphics, stats, BiocParallel Suggests: testthat Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 9382700c66a2d4d36b9009a8432126a5 Package: terraTCGAdata Version: 1.8.0 Depends: R (>= 4.2.0), AnVIL, MultiAssayExperiment Imports: BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils Suggests: knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 560a8280f98dce5985208c270b38627f Package: TFARM Version: 1.26.0 Depends: R (>= 3.5.0) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: c10d1df454e242fda5266e9033781747 Package: TFEA.ChIP Version: 1.24.0 Depends: R (>= 3.5) Imports: GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 MD5sum: c262eaa11c2af1723308014b9844781b Package: TFHAZ Version: 1.26.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods, ORFik Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1d77878932bb691f6a575a86baa3709e Package: TFutils Version: 1.24.0 Depends: R (>= 4.1.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: 96bde8a8967880d684d2475684471e31 Package: tidybulk Version: 1.16.0 Depends: R (>= 4.1.0), ttservice (>= 0.3.6) Imports: tibble, readr, dplyr (>= 1.1.0), magrittr, tidyr, stringi, stringr, rlang, purrr, tidyselect, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon, Matrix Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig License: GPL-3 MD5sum: 740c4b28b87258c5c3e37a8d2facc598 Package: tidyCoverage Version: 1.0.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, dplyr, fansi, pillar, rlang, cli, purrr, vctrs, stats Suggests: tidySummarizedExperiment, plyranges, ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a0a1c11331d089c6de1726325c4d16ca Package: tidyomics Version: 1.0.0 Depends: R (>= 4.2) Imports: tidySummarizedExperiment, tidySingleCellExperiment, tidyseurat, tidybulk, plyranges, nullranges, purrr, rlang, stringr, cli, utils Suggests: tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6) License: MIT + file LICENSE MD5sum: e0d06179058a654b8383b6f20e609649 Package: tidySingleCellExperiment Version: 1.14.0 Depends: R (>= 4.3.0), SingleCellExperiment Imports: dplyr, tidyr, ttservice (>= 0.4.0), SummarizedExperiment, tibble, ggplot2, magrittr, rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, Matrix, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly License: GPL-3 MD5sum: 9268b36c72f133f632be16f012f3cb2f Package: tidySpatialExperiment Version: 1.0.0 Depends: R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment Imports: ttservice, SummarizedExperiment, SingleCellExperiment, BiocGenerics, Matrix, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2, magrittr, rlang, purrr, stringr, vctrs, tidyselect, pillar, cli, fansi, lifecycle Suggests: BiocStyle, testthat, knitr, markdown, SingleCellSignalR, SingleR, scater, scran, igraph, GGally, celldex, dittoSeq, cowplot, DropletUtils, plotly, tidySummarizedExperiment License: GPL-3 MD5sum: e623b97900208b19d2bea0733be73292 Package: tidySummarizedExperiment Version: 1.14.0 Depends: R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.4.0) Imports: dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig Suggests: BiocStyle, testthat, knitr, markdown, plotly License: GPL-3 MD5sum: 418b6c9d59808b181a27671bdddef88c Package: tigre Version: 1.58.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: a8f2d608c94e5cb4e3a4d92f9feec449 Package: TileDBArray Version: 1.14.0 Depends: DelayedArray (>= 0.27.2) Imports: methods, Rcpp, tiledb, S4Vectors LinkingTo: Rcpp Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: b0da8a6d879f5d3fb1ff6b6b5621a72c Package: tilingArray Version: 1.82.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: 6e3bc2f2fe4c4bfe47da35d574864ac5 Package: timecourse Version: 1.76.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 65916da4a1cae46252d3c05e449209e6 Package: timeOmics Version: 1.16.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, lmtest, plyr, checkmate Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: f004916f0f059357ce03a0c850396f9a Package: timescape Version: 1.28.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 7e3374290b533dcb4aa209e42ba19eb9 Package: TIN Version: 1.36.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: ed19f6f7a7dbb93f7db2f99227637d6a Package: TissueEnrich Version: 1.24.1 Depends: R (>= 3.5), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 5d8091b97642a4976148933b58d56cf2 Package: TitanCNA Version: 1.42.0 Depends: R (>= 3.5.1) Imports: BiocGenerics (>= 0.31.6), IRanges (>= 2.6.1), GenomicRanges (>= 1.24.3), VariantAnnotation (>= 1.18.7), foreach (>= 1.4.3), GenomeInfoDb (>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0), License: GPL-3 MD5sum: bbcc3f836809ab42be61f88142b8ac56 Package: tkWidgets Version: 1.82.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: 58973adedde99977787d356f016cca71 Package: tLOH Version: 1.12.0 Depends: R (>= 4.2) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 403106b7eecd8448aa701458f066f493 Package: TMixClust Version: 1.26.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) MD5sum: 011850cf72d05d63e0f9fbdba1543776 Package: TOAST Version: 1.18.0 Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix License: GPL-2 MD5sum: 089596905ff94767ec2510c15cc90975 Package: tomoda Version: 1.14.0 Depends: R (>= 4.0.0) Imports: methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 842bf115fc99321b6edd0d6110620adc Package: tomoseqr Version: 1.8.0 Depends: R (>= 4.2) Imports: grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2 Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 21647155422cb035fcff9e6a8a20d17f Package: TOP Version: 1.4.0 Depends: R (>= 3.5.0) Imports: assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 MD5sum: c2b266de7fc57f48c702d9980e897926 Package: topconfects Version: 1.20.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2 Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE MD5sum: 5b0d83b9db24544df6a82e946e81baba Package: topdownr Version: 1.26.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase (>= 2.3.10), PSMatch (>= 1.6.0), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: a2df5aa7ee853f75b7e1ca0454641cda Package: topGO Version: 2.56.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL MD5sum: c04ddd8a704875d3fa07d316bff43162 Package: ToxicoGx Version: 2.8.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE MD5sum: a5d64125a5aa890a033d66730a1a86b4 Package: TPP2D Version: 1.20.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: dbc9d47dcdbeae833ea27ebf9a322cf8 Package: TPP Version: 3.32.0 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 9b2d70d4f642a0398f78940a7b73fd26 Package: tpSVG Version: 1.0.0 Depends: mgcv, R (>= 4.4) Imports: stats, BiocParallel, MatrixGenerics, methods, SingleCellExperiment, SummarizedExperiment, SpatialExperiment Suggests: BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: b9a8a4460aed576335b00da152402a72 Package: tracktables Version: 1.38.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: 3f1ec896de0c8222103f2621080a934a Package: trackViewer Version: 1.40.0 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, InteractionSet, igraph, utils, rhdf5, strawr, txdbmaker Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: 68d49cad35ab9d2ffbc4ee3a2b9174a3 Package: tradeSeq Version: 1.18.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats License: MIT + file LICENSE MD5sum: 7e7ede428fcf5e9a115c1dfeeb8f0f61 Package: TrajectoryGeometry Version: 1.12.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: 9aa06f039dc6327d0fc9780975c5d351 Package: TrajectoryUtils Version: 1.12.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 6e82a9bf7097544f1b05306461781c67 Package: transcriptogramer Version: 1.26.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 14c40b815e9ad89401f7fa4e7402960b Package: transcriptR Version: 1.32.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: 8b0d4d108eb4802b3fbde7191635a910 Package: transformGamPoi Version: 1.10.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 6bc0379f07efef5702e24a38b5929926 Package: transite Version: 1.22.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 199ec18b7bf73726d58d195ee35fffc3 Package: tRanslatome Version: 1.42.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: e872c10acc571cdd364182b7d3d20f24 Package: transmogR Version: 1.0.0 Depends: Biostrings, GenomicRanges Imports: BSgenome, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, methods, parallel, rlang, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, ComplexUpset, extraChIPs, InteractionSet, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 MD5sum: 8b4fe2724524fda85998b90507d2cead Package: transomics2cytoscape Version: 1.14.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 94a638c76ca8b21ade0dff5589ee5993 Package: TransView Version: 1.48.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.99.1) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: 1b52bc82de1296cf7c21802c6d4979ef Package: traseR Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: cbcfdf1441b206908d1d298f9c3eb9b8 Package: traviz Version: 1.10.0 Depends: R (>= 4.0) Imports: ggplot2, viridis, mgcv, SingleCellExperiment, slingshot, princurve, Biobase, methods, RColorBrewer, SummarizedExperiment, grDevices, graphics, rgl Suggests: scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr License: MIT + file LICENSE MD5sum: 2e86db5c89fec096bc4790ba7336096d Package: TreeAndLeaf Version: 1.16.0 Depends: R(>= 4.0) Imports: RedeR(>= 1.40.4), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 MD5sum: 4adc98f47ef33bb385c836119daaf6d1 Package: treeclimbR Version: 1.0.0 Depends: R (>= 4.4.0) Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: 81ea49b7db6cb5ea2bd13605163c174e Package: treeio Version: 1.28.0 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (> 0.1.1) Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: 03c2d32d6fe7bdb4730b07126722a80f Package: treekoR Version: 1.12.0 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 MD5sum: f4563c1b4d55cbc0ba376d5fb86b7a24 Package: TreeSummarizedExperiment Version: 2.12.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: fb93381f90c9c34e6d6eab4c617a24ae Package: TREG Version: 1.8.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 MD5sum: 2750bb8a4014f81c77c150aa86bc009f Package: Trendy Version: 1.26.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: e680003aba30f471d7720f938a58cce4 Package: TRESS Version: 1.10.0 Depends: R (>= 4.1.0), parallel, S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: 9ee0f72b76a9bc10b56b23704fd9b908 Package: tricycle Version: 1.12.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 6be47c9021347e2ec5447aa22f8decf5 Package: trigger Version: 1.50.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: 5de9004c77dba1cd3284eeaf1f668341 Package: trio Version: 3.42.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: 2a1071a581e8de5f199aa3ff316de9b4 Package: triplex Version: 1.44.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: 057448de040844b751a2624a54811a07 Package: tripr Version: 1.10.0 Depends: shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE MD5sum: d39ff7a77dd46f922ec43f62abbf453f Package: tRNA Version: 1.22.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: 7860a7ab3b9f578e006191024d96d25c Package: tRNAdbImport Version: 1.22.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: 477018c1c8fb2a23a5be9c6bb1992ea5 Package: tRNAscanImport Version: 1.24.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 99dff493e8b9d0d6421295d3bec93dd0 Package: TRONCO Version: 2.36.0 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 MD5sum: 0fd8d95dfa7e18ce61de41ca741e477a Package: TSAR Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: fa2ba8ca581c93926d617bfa743ab931 Package: TSCAN Version: 1.42.0 Depends: SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, DelayedArray, S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: 643e650b3ead7303c9bbd123ad7388be Package: ttgsea Version: 1.12.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 06514967b0464d77d05f2b7cfeb6d6db Package: TTMap Version: 1.26.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: b5e103a33dbff16c4a66c057a6053b42 Package: TurboNorm Version: 1.52.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL MD5sum: 0a119b46b4d4d45d6c37c39f60b83633 Package: TVTB Version: 1.30.1 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 503ba7cdd36962ebeabbb78d67111fbe Package: tweeDEseq Version: 1.50.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils LinkingTo: Rcpp Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 18ee1ca6f7427aa2d6e2c6fa9b11f49d Package: twilight Version: 1.80.0 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) MD5sum: 878cdd600d7691868924cc5af9b61229 Package: twoddpcr Version: 1.28.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 26232674ec1727326b37f7185dd5923c Package: txcutr Version: 1.10.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 MD5sum: fec6da2015fec89511d753117c567dae Package: txdbmaker Version: 1.0.1 Depends: BiocGenerics, S4Vectors, GenomeInfoDb (>= 1.39.9), GenomicRanges, GenomicFeatures Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) Suggests: RMariaDB, mirbase.db, ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 17643ace5387bb5a248ce8e51a4c43ab Package: tximeta Version: 1.22.1 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools License: GPL-2 MD5sum: c9b2f101d2fe2db40255b8c1cd7bffa8 Package: tximport Version: 1.32.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: 32294b485754c1b1fbb7b8c605564b9e Package: UCell Version: 2.8.0 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 6820f343c316bdb0939c29ccf53e2ba0 Package: UCSC.utils Version: 1.0.0 Imports: methods, stats, httr, jsonlite, S4Vectors Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b746031dd3dccef66d2c28db3ceedcef Package: Ularcirc Version: 1.22.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: d64b7c785b305758be73396db8c9ab15 Package: UMI4Cats Version: 1.14.0 Depends: R (>= 4.0.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: d0515ac0385f39689db9b20a0166d9dc Package: uncoverappLib Version: 1.14.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: c62a00bb25d182be40b61200b7b9487b Package: UNDO Version: 1.46.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: a3fb7aac7787cc651b89c67ad6e73322 Package: UniProt.ws Version: 2.44.0 Depends: BiocGenerics, methods, RSQLite, utils Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, httr, httpcache, jsonlite, progress, rjsoncons Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 6b8aa1686bec74f287193fc88b1f72c8 Package: Uniquorn Version: 2.24.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table Suggests: testthat, knitr, rmarkdown, BiocGenerics License: Artistic-2.0 MD5sum: 47f5143499e0a34611f01ffbbfd058fb Package: universalmotif Version: 1.22.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: 61560f08763ed6cd23087088a1094f79 Package: updateObject Version: 1.8.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.47.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, TimiRGeN, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: e00e71e4d8ca4810a8cc2cd99c201037 Package: UPDhmm Version: 1.0.0 Depends: R (>= 4.3.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, stats Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr License: MIT + file LICENSE MD5sum: 283af86c3fbff5fd7cc35d852df38a48 Package: uSORT Version: 1.30.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: 64d2f782c892a7a8a47cd3c787446075 Package: VAExprs Version: 1.10.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 82ec91573022022cb6e2c3bcd19e5990 Package: VanillaICE Version: 1.66.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 89ae5dd6d2c25d469bf75cd2d2445b81 Package: VarCon Version: 1.12.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: c2093c27fc6bb8e04d54f00f98a5e632 Package: variancePartition Version: 1.34.0 Depends: R (>= 4.3.0), ggplot2, limma, BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: b72bc834061652282e80b4c16c1079a8 Package: VariantAnnotation Version: 1.50.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 2.19.1) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: cb8e485b91b25651823e60e9c890be32 Package: VariantFiltering Version: 1.40.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: cb7a424c2da5a7300c971c5cb8ed3ee4 Package: VariantTools Version: 1.46.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: Artistic-2.0 MD5sum: 5be48f9d8e210b65212482db8826acfd Package: VaSP Version: 1.16.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: fe11312ba64d98a64387aef03d0095f9 Package: vbmp Version: 1.72.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 57c950f0d276e3bfa39e541b8ee38c75 Package: VCFArray Version: 1.20.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: e2bd427bb5f1091d8cc4473ca9ec734b Package: VDJdive Version: 1.6.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 2c602f5d6c29d21f5272d5fb7d4b3c3d Package: VegaMC Version: 3.42.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: 90c49283057c0ac01c41d50881bbe624 Package: velociraptor Version: 1.14.3 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR License: MIT + file LICENSE MD5sum: febb80d7f1420a83632a8f2c6705d615 Package: veloviz Version: 1.10.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8f9d770d51a483c43773a9898ed7c326 Package: VennDetail Version: 1.20.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 MD5sum: 71b5c0fb1994a5f87fec16aa41b03168 Package: VERSO Version: 1.14.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: edfee3882e531703fd3131e7b20a06ca Package: vidger Version: 1.24.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: bb79d332240a9cd84a5f0d8f46d05043 Package: viper Version: 1.38.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: 3314fd197e450c19a72b28f6a2a2b846 Package: ViSEAGO Version: 1.18.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, processx, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager MD5sum: f47a7270795cb937d94fab80ba85f325 Package: VisiumIO Version: 1.0.0 Depends: R (>= 4.4.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods, S4Vectors, SpatialExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 5807f7031c43ae0f1f06f471b856bb84 Package: vissE Version: 1.12.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: de2730276d0d14a9c14f9378932261e5 Package: Voyager Version: 1.6.0 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.5.2) Imports: BiocParallel, bluster, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, matrixStats, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils Suggests: automap, BiocSingular, BiocStyle, cowplot, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom, xml2 License: Artistic-2.0 MD5sum: 92efebe2f82cb5a540cf4f03660101e2 Package: VplotR Version: 1.14.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: 6aee848574a406a8937768cefcf1bb0d Package: vsclust Version: 1.6.0 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler License: GPL-2 MD5sum: 1dd8ea068794b16f339fd922350cd38d Package: vsn Version: 3.72.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: b0563ec5efe53c5bc507936664a12b45 Package: vtpnet Version: 0.44.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: a268648369cd8215cfaae5d3b16d9375 Package: vulcan Version: 1.26.0 Depends: R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: 18a35478892f37c4f890054c78139126 Package: wateRmelon Version: 2.10.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 MD5sum: 027149e3ea9f3dccfa1ff27951636ad2 Package: wavClusteR Version: 2.38.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: 0ea6b0dfa57e6e6997eccc668d049a33 Package: weaver Version: 1.70.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 6fad5c5d363c53f69d3a3f4dabe27af0 Package: webbioc Version: 1.76.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: 1797b273c9c17c6f8f8f60cdf7d41895 Package: weitrix Version: 1.16.0 Depends: R (>= 3.6), SummarizedExperiment Imports: methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: 6b9ad0a3acdfd95c0b7a23743c14a593 Package: widgetTools Version: 1.82.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 0240f6ff19c4f17add0e9fc7db85028a Package: wiggleplotr Version: 1.28.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 MD5sum: 4b9cabebc466cd6887acc237b8896882 Package: wpm Version: 1.14.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: b1b59cc1d62b7bf29ac0f67e2e49592b Package: wppi Version: 1.12.0 Depends: R(>= 4.1) Imports: dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr Suggests: knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: 3f267030dbd1e3e8f5b93e3e1ddb5217 Package: Wrench Version: 1.22.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: bcd58ac94d88b765e1e7e55419545517 Package: xcore Version: 1.8.0 Depends: R (>= 4.2) Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>= 1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>= 1.18.0), stats, S4Vectors (>= 0.30.0), utils Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata License: GPL-2 MD5sum: 0584a514c77dfec31764481e701b8549 Package: XDE Version: 2.50.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: 65158042affc4c5e11c78480b983128e Package: Xeva Version: 1.20.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: a53ec43c0acc994c7676b3e34e924f06 Package: XINA Version: 1.22.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: a3cde80a87ef57300b1853445fcefeda Package: xmapbridge Version: 1.62.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: e58944a5d2bb00c83d112c7ee319e9b5 Package: XNAString Version: 1.12.0 Depends: R (>= 4.1) Imports: utils, Biostrings, pwalign, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander License: GPL-2 MD5sum: 604971d1ce70279350ab03f6fa19ba45 Package: XVector Version: 0.44.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9) Imports: methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: c3f33af5705eff7f27272abc9f2c24b4 Package: yamss Version: 1.30.0 Depends: R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: 30238771059d4d5239e23d0b1b62819d Package: YAPSA Version: 1.30.0 Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 3837cfde06136f8f3e22e39c7a7086ee Package: yarn Version: 1.30.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: 499c8c6d59120143bc7dbb199131f6a5 Package: zellkonverter Version: 1.14.1 Imports: Matrix, basilisk, reticulate, SingleCellExperiment (>= 1.11.6), SummarizedExperiment, DelayedArray, methods, S4Vectors, utils, cli Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5 (>= 2.45.1), scRNAseq, spelling, testthat, withr License: MIT + file LICENSE MD5sum: 832845be54f1eadd4da02eb8aebf5d6c Package: zenith Version: 1.6.0 Depends: R (>= 4.2.0), limma, methods Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 MD5sum: 19be23c1d715d31d898822b030fecdbc Package: zFPKM Version: 1.26.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: ed1879b06c5e9edb3e75ca2551a88129 Package: zinbwave Version: 1.26.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats License: Artistic-2.0 MD5sum: 3b6c91aa11f53632f6303082903eeb8c Package: zlibbioc Version: 1.50.0 Suggests: BiocStyle, knitr License: Artistic-2.0 + file LICENSE MD5sum: a11edd6bad3f2404450a27c338d1e884 Package: ZygosityPredictor Version: 1.4.0 Depends: R (>= 4.3.0) Imports: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, igraph, readr, stats, magrittr, rlang Suggests: rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 4e8e8ddb21ca15047e96ec2a29fae514