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gplots, R2HTML, oligoClasses, ReportingTools, hwriter Suggests: affydata, hgfocuscdf, rgl License: Artistic-2.0 Package: AffyExpress Version: 1.26.0 Depends: R (>= 2.10), affy (>= 1.23.4), limma Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma License: LGPL Package: affyILM Version: 1.12.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, methods, Biobase Suggests: AffymetrixDataTestFiles License: GPL-3 Package: affyio Version: 1.28.0 Depends: R (>= 2.6.0), methods Imports: zlibbioc License: LGPL (>= 2) Archs: i386, x64 Package: affylmGUI Version: 1.34.0 Depends: limma, tcltk, affy, BiocInstaller, affyio, affy, tkrplot, affyPLM, R2HTML, xtable, gcrma, affyPLM, AnnotationDbi License: LGPL Package: affyPara Version: 1.20.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0), aplpack (>= 1.1.1), affyio Suggests: affydata Enhances: affy License: GPL-3 Package: 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multtest, tcltk License: LGPL Package: annotate Version: 1.38.0 Depends: R (>= 2.10), AnnotationDbi (>= 0.1.15) Imports: Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats, methods, XML (>= 0.92-2), BiocGenerics (>= 0.1.13) Suggests: Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.25.10), rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, XML (>= 0.92-2), org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, License: Artistic-2.0 Package: AnnotationDbi Version: 1.22.6 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.5.4), Biobase (>= 1.17.0) Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase, IRanges Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, seqnames.db, reactome.db, AnnotationForge, graph License: Artistic-2.0 Package: AnnotationForge Version: 1.2.2 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 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GOstats, graphics, methods, stats Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) Package: BAC Version: 1.20.0 Depends: R (>= 2.10) License: Artistic-2.0 Archs: i386, x64 Package: BaseSpaceR Version: 1.0.1 Depends: R (>= 2.15.0), methods, RCurl, RJSONIO Imports: methods Suggests: RUnit License: Apache License 2.0 Package: BayesPeak Version: 1.12.0 Depends: R (>= 2.14), IRanges Imports: IRanges, graphics License: GPL (>= 2) Archs: i386, x64 Package: baySeq Version: 1.14.1 Depends: R (>= 2.3.0), methods Suggests: snow, edgeR License: GPL-3 Package: BCRANK Version: 1.22.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 Archs: i386, x64 Package: beadarray Version: 2.10.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), methods, ggplot2 Imports: BeadDataPackR, limma, AnnotationDbi, stats4, BiocGenerics, reshape2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra License: GPL-2 Archs: i386, x64 Package: 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Depends: R (>= 2.3.0), minet Imports: stats License: GPL-3 Archs: i386, x64 Package: CAGEr Version: 1.2.9 Depends: methods, R (>= 2.15.0), BSgenome, BSgenome.Mmusculus.UCSC.mm9 Imports: Rsamtools, GenomicRanges, IRanges, data.table, beanplot, rtracklayer, som, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, FANTOM3and4CAGE Enhances: parallel License: GPL-3 Package: CALIB Version: 1.26.0 Depends: R (>= 2.10), limma, methods Imports: limma, methods, graphics, stats, utils License: LGPL Archs: i386, x64 Package: CAMERA Version: 1.16.0 Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5), igraph Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics Enhances: Rmpi, snow License: GPL (>= 2) Archs: i386, x64 Package: cancerclass Version: 1.4.0 Depends: R (>= 2.10.1), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 Archs: i386, x64 Package: CancerMutationAnalysis Version: 1.4.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE Archs: i386, x64 Package: casper Version: 1.1.2 Depends: R (>= 2.14.1), Biobase, IRanges, methods, gtools, GenomicRanges, Rsamtools, plyr, gaga Imports: VGAM, mgcv, GenomicFeatures, survival, sqldf Enhances: parallel License: GPL (>= 2) Archs: i386, x64 Package: Category Version: 2.26.0 Depends: BiocGenerics (>= 0.3.2), AnnotationDbi (>= 0.1.15), Biobase (>= 2.17.8), methods Imports: BiocGenerics, graph, methods, Biobase, AnnotationDbi, RBGL, GSEABase (>= 1.19.3), genefilter, annotate (>= 1.15.6), stats, utils Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, Matrix, KEGG.db, GO.db, SNPchip (>= 2.3.11), geneplotter, limma, lattice, graph, Biobase, genefilter, methods, RUnit, org.Sc.sgd.db, GOstats License: Artistic-2.0 Package: categoryCompare Version: 1.4.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), AnnotationDbi (>= 0.1.15), Category (>= 2.23.4) Imports: BiocGenerics, Biobase, AnnotationDbi, hwriter, GSEABase, Category, GOstats, annotate, colorspace, graph, RCytoscape (>= 1.5.11) Suggests: methods, GSEABase, hwriter, colorspace, graph, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter License: GPL-2 Package: cellGrowth Version: 1.4.0 Depends: R (>= 2.12.0), locfit (>= 1.5-4) Imports: lattice License: Artistic-2.0 Package: cellHTS Version: 1.30.0 Depends: R (>= 2.10), prada (>= 1.9.4), RColorBrewer, Biobase (>= 1.11.12), genefilter (>= 1.11.2) Suggests: Category, GO.db, vsn (>= 2.0.35) License: Artistic-2.0 Package: cellHTS2 Version: 2.24.1 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: prada, GSEABase, Category, stats4 License: Artistic-2.0 Package: CellNOptR Version: 1.6.0 Depends: R (>= 2.15.0), RBGL, graph, methods, hash, ggplot2, RCurl, Rgraphviz Suggests: RUnit, BiocGenerics, igraph License: GPL-2 Archs: i386, x64 Package: CGEN Version: 2.2.0 Depends: R (>= 2.10.1), survival Suggests: cluster License: GPL-2 + file LICENSE Archs: i386, x64 Package: CGHbase Version: 1.20.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL Package: CGHcall Version: 2.20.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall License: GPL Package: cghMCR Version: 1.18.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL Package: CGHnormaliter Version: 1.14.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) Package: CGHregions Version: 1.18.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase License: GPL Package: charm Version: 2.6.0 Depends: R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter Imports: BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses(>= 1.17.39), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils, limma, parallel, sva(>= 3.1.2) Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor License: LGPL (>= 2) Package: ChemmineR Version: 2.12.3 Depends: R (>= 2.10.0), methods Imports: graphics, methods, stats, RCurl, DBI, digest, BiocGenerics Suggests: RSQLite, scatterplot3d, gplots, fmcsR License: Artistic-2.0 Archs: i386, x64 Package: chimera Version: 1.2.6 Depends: Biobase, GenomicRanges, Rsamtools, methods, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene Enhances: Rsubread License: Artistic-2.0 Package: ChIPpeakAnno Version: 2.8.0 Depends: R (>= 2.10), grid,VennDiagram, BiocGenerics (>= 0.1.0), biomaRt, multtest, IRanges, Biostrings, BSgenome, BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma, GenomicFeatures Imports: gplots, BiocGenerics, biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db, limma, AnnotationDbi, GenomicFeatures Suggests: reactome.db, RUnit, BiocGenerics License: GPL (>= 2) Package: chipseq Version: 1.10.1 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.4), GenomicRanges (>= 1.7.7), BSgenome, ShortRead Imports: methods, BiocGenerics, IRanges, BSgenome, GenomicRanges, lattice, ShortRead, stats Suggests: GenomicFeatures, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene License: Artistic-2.0 Archs: i386, x64 Package: ChIPseqR Version: 1.14.0 Depends: R (>= 2.10.0), methods, BiocGenerics, ShortRead Imports: Biostrings, fBasics, GenomicRanges, graphics, grDevices, HilbertVis, IRanges, methods, ShortRead, stats, timsac, utils License: GPL (>= 2) Archs: i386, x64 Package: ChIPsim Version: 1.14.0 Depends: Biostrings Imports: IRanges, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) Package: chopsticks 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graph Imports: methods, Biobase, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL Suggests: RUnit, BiocGenerics, RCytoscape (>= 1.6.3), graphite, ALL, hgu95av2.db License: AGPL-3 Package: Clonality Version: 1.8.0 Depends: R (>= 2.12.2), DNAcopy Imports: DNAcopy, grDevices, graphics, stats, utils Suggests: gdata, DNAcopy License: GPL-3 Package: clst Version: 1.8.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 Package: clstutils Version: 1.8.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit, RSVGTipsDevice License: GPL-3 Package: clusterProfiler Version: 1.8.0 Depends: R (>= 2.10), ggplot2 Imports: methods, stats4, DBI, plyr, AnnotationDbi, GO.db, KEGG.db, org.Hs.eg.db, DOSE Suggests: GOSemSim, ReactomePA License: Artistic-2.0 Package: clusterStab Version: 1.32.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 Package: CMA Version: 1.18.0 Depends: R (>= 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GPL-2 Package: coGPS Version: 1.4.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 Package: ConsensusClusterPlus Version: 1.16.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 Package: convert Version: 1.36.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL Package: copa Version: 1.28.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 Archs: i386, x64 Package: copynumber Version: 1.1.1 Depends: R (>= 2.10), BiocGenerics Imports: GenomicRanges, IRanges License: Artistic-2.0 Package: Cormotif Version: 1.6.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 Package: CorMut Version: 1.2.0 Depends: methods, Biostrings, seqinr,igraph License: GPL-2 Package: coRNAi Version: 1.10.1 Depends: R (>= 2.10), cellHTS2, limma, locfit Imports: MASS, gplots, lattice, grDevices, graphics, stats License: Artistic-2.0 Package: CORREP Version: 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Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 Package: DEGseq Version: 1.14.0 Depends: R (>= 2.8.0), qvalue, samr, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) Archs: i386, x64 Package: deltaGseg Version: 1.0.3 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 Package: DESeq Version: 1.12.1 Depends: Biobase (>= 2.13.11), locfit, lattice Imports: genefilter, geneplotter, methods, MASS, RColorBrewer Suggests: pasilla (>= 0.2.10), vsn, gplots License: GPL (>= 3) Archs: i386, x64 Package: DESeq2 Version: 1.0.19 Depends: GenomicRanges, IRanges, Biobase, lattice, Rcpp (>= 0.10.1), RcppArmadillo (>= 0.3.4.4) Imports: GenomicRanges, IRanges, Biobase, locfit, genefilter, methods, RColorBrewer, lattice LinkingTo: 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0.1.3), Biobase (>= 2.15.1), ShortRead (>= 1.11.42), Rsamtools (>= 1.5.75), aroma.light Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq Suggests: yeastRNASeq, leeBamViews, edgeR, DESeq License: Artistic-2.0 Package: edgeR Version: 3.2.4 Depends: R (>= 2.15.0), methods, limma Suggests: MASS, statmod, splines, locfit, KernSmooth License: GPL (>= 2) Archs: i386, x64 Package: eisa Version: 1.12.2 Depends: isa2, Biobase (>= 2.17.8), AnnotationDbi, methods Imports: BiocGenerics, Category, genefilter, DBI Suggests: igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db License: GPL (>= 2) Package: ensemblVEP Version: 1.0.5 Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation Imports: Biostrings, IRanges Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: ENVISIONQuery Version: 1.8.1 Depends: rJava, XML, utils License: GPL-2 Package: epigenomix Version: 1.0.1 Depends: R (>= 2.12.0), 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Depends: R (>= 2.8.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) Archs: i386, x64 Package: factDesign Version: 1.36.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL Package: farms Version: 1.12.0 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) Package: fastseg Version: 1.6.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: graphics, stats, IRanges, BiocGenerics Suggests: DNAcopy, oligo License: LGPL (>= 2.0) Archs: i386, x64 Package: fdrame Version: 1.32.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: ffpe Version: 1.4.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, affy, ffpeExampleData License: GPL (> 2) Package: flagme Version: 1.16.2 Depends: gcspikelite, xcms Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) Archs: i386, x64 Package: flowClust Version: 3.0.0 Depends: R(>= 2.5.0),methods, Biobase, graph, RBGL,ellipse, flowViz, mnormt, corpcor, flowCore(>= 1.11.23), clue Imports: BiocGenerics, MCMCpack Suggests: parallel License: Artistic-2.0 Archs: i386, x64 Package: flowCore Version: 1.26.3 Depends: R (>= 2.10.0), Biobase, rrcov Imports: Biobase, BiocGenerics (>= 0.1.14), feature, graph, graphics, grDevices, MASS, methods, rrcov, stats, utils, stats4 Suggests: Rgraphviz, flowViz, ncdf License: Artistic-2.0 Archs: i386, x64 Package: flowFlowJo Version: 1.18.0 Depends: R (>= 2.5.0), MASS, Imports: flowCore, XML (>= 1.96), methods, Biobase License: GPL (>= 3) Package: flowFP Version: 1.18.0 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), flowCore, flowViz, graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 Archs: i386, x64 Package: flowMeans Version: 1.12.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 Package: flowMerge Version: 2.8.0 Depends: Rgraphviz, flowClust, flowCore, methods,snow,foreach,graph,feature Imports: rrcov, flowClust,flowCore, graphics, methods, rrcov, stats, utils, BiocGenerics (>= 0.1.6) Suggests: Rgraphviz Enhances: doMC, multicore License: Artistic-2.0 Package: flowPeaks Version: 1.2.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 Archs: i386, x64 Package: flowPhyto Version: 1.12.1 Depends: R (>= 1.8.0) Imports: flowClust, flowCore, flowMeans, TTR Suggests: RPostgreSQL, zoo, maps, mapdata, plotrix License: Artistic-2.0 Package: flowPlots Version: 1.8.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 Package: flowQB Version: 1.2.0 Imports: Biobase, graphics,methods, flowCore,stats Suggests: flowCore License: Artistic-2.0 Package: flowTrans Version: 1.12.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 Package: flowType Version: 1.6.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, flowCore, flowMeans, sfsmisc, rrcov, flowClust, flowMerge, stats Suggests: xtable License: Artistic-2.0 Package: flowUtils Version: 1.20.0 Depends: R (>= 2.2.0), flowCore (>= 1.2.0) Imports: Biobase, flowCore, graph, methods, RUnit, stats, utils, XML, flowViz Suggests: gatingMLData License: Artistic-2.0 Package: flowViz Version: 1.24.0 Depends: R (>= 2.7.0), flowCore (>= 1.5.17), lattice, grDevices Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace,RColorBrewer License: Artistic-2.0 Package: fmcsR Version: 1.2.1 Depends: R (>= 2.10.0), ChemmineR, methods License: Artistic-2.0 Archs: i386, x64 Package: frma Version: 1.12.0 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) Package: frmaTools Version: 1.12.0 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) Package: FunciSNP Version: 1.2.0 Depends: R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data Imports: AnnotationDbi, IRanges, Rsamtools (>= 1.6.1), rtracklayer(>= 1.14.1), methods, ChIPpeakAnno (>= 2.2.0), GenomicRanges, VariantAnnotation, plyr, org.Hs.eg.db, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales Enhances: parallel License: GPL-3 Package: gaga Version: 2.6.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: multicore License: GPL (>= 2) Archs: i386, x64 Package: gage Version: 2.10.0 Depends: R (>= 2.10) Imports: graph Suggests: pathview, gageData, GO.db, KEGG.db, org.Hs.eg.db, hgu133a.db, GSEABase License: GPL (>= 2.0) Package: gaggle Version: 1.28.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) Package: gaia Version: 2.4.0 Depends: R (>= 2.10) License: GPL-2 Package: gcrma Version: 2.32.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), IRanges, Biostrings (>= 2.11.32), splines, BiocInstaller Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL Archs: i386, x64 Package: genArise Version: 1.36.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes Package: GeneAnswers Version: 2.2.1 Depends: R (>= 2.10.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer Imports: RBGL, annotate Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph License: LGPL (>= 2) Package: GENE.E Version: 1.1.0 Depends: R (>= 2.7.0), h5r (>= 1.4.1), RCurl (>= 1.6-6) Imports: h5r, RCurl Suggests: RUnit, BiocGenerics, knitr, golubEsets (>= 1.0) License: GPL-2 Package: GeneExpressionSignature Version: 1.6.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 Package: genefilter Version: 1.42.0 Imports: AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10), graphics, methods, stats, survival Suggests: Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets, ALL, ROC, DESeq, pasilla License: Artistic-2.0 Archs: i386, x64 Package: genefu Version: 1.10.0 Depends: R (>= 2.10), survcomp, mclust, biomaRt Imports: amap Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable License: Artistic-2.0 Package: GeneGroupAnalysis Version: 1.6.0 Depends: R (>= 2.10), MCMCpack, GO.db, breastCancerVDX, rheumaticConditionWOLLBOLD, hgu133a.db, hgu133plus2.db Imports: AnnotationDbi, annotate, tcltk License: Artistic-2.0 Archs: i386, x64 Package: GeneMeta Version: 1.32.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 Package: GeneNetworkBuilder Version: 1.2.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13), graph Imports: plyr, graph LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, Rgraphviz, XML, RCytoscape License: GPL (>= 2) Archs: i386, x64 Package: geneplotter Version: 1.38.0 Depends: R (>= 2.10),Biobase (>= 2.5.5), annotate, lattice Imports: annotate, AnnotationDbi, Biobase (>= 2.5.5), graphics, grDevices, grid, methods, RColorBrewer, stats, utils Suggests: Biobase (>= 2.5.5), Rgraphviz, annotate, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 Package: geneRecommender Version: 1.32.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) Package: GeneRegionScan Version: 1.16.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) Package: GeneSelectMMD Version: 2.4.0 Depends: R (>= 2.13.2), Biobase Imports: Biobase, MASS, graphics, stats, survival, limma Suggests: ALL License: GPL (>= 2) Archs: i386, x64 Package: GeneSelector Version: 2.10.0 Depends: R (>= 2.5.1), methods, stats, Biobase Imports: multtest, siggenes, samr, limma Suggests: multtest, siggenes, samr, limma License: GPL (>= 2) Archs: i386, x64 Package: geNetClassifier Version: 1.0.2 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, ipred, graphics, BiocGenerics Suggests: leukemiasEset Enhances: 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pasilla, pasillaBamSubset, org.Sc.sgd.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, seqnames.db, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Dmelanogaster.UCSC.dm3, RUnit, digest License: Artistic-2.0 Archs: i386, x64 Package: Genominator Version: 1.14.0 Depends: R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics (>= 0.1.0), IRanges, GenomeGraphs Imports: graphics, stats, utils Suggests: biomaRt, ShortRead, yeastRNASeq License: Artistic-2.0 Package: genoset Version: 1.12.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.6), Biobase (>= 2.15.1), IRanges (>= 1.13.5), GenomicRanges Imports: methods, graphics, GenomicRanges Suggests: RUnit, DNAcopy, stats Enhances: parallel License: Artistic-2.0 Archs: i386, x64 Package: GEOmetadb Version: 1.20.0 Depends: GEOquery,RSQLite License: Artistic-2.0 Package: GEOquery Version: 2.26.2 Depends: methods, Biobase Imports: XML, RCurl Suggests: limma License: GPL-2 Package: GEOsubmission Version: 1.12.0 Imports: affy, Biobase, utils License: GPL (>= 2) Package: GEWIST Version: 1.4.0 Depends: R (>= 2.10), car License: GPL-2 Package: GGBase Version: 3.22.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, Matrix, AnnotationDbi License: Artistic-2.0 Package: ggbio Version: 1.8.8 Depends: methods, ggplot2 (>= 0.9.2) Imports: methods, biovizBase(>= 1.7.8), reshape2, gtable, ggplot2(>= 0.9.2), BiocGenerics, Biobase, IRanges, GenomicRanges, GenomicFeatures, Rsamtools, BSgenome, gridExtra, scales, plyr, VariantAnnotation, Hmisc, rtracklayer Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, affyPLM, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr License: Artistic-2.0 Package: GGtools Version: 4.8.0 Depends: R (>= 2.14), stats4, GGBase (>= 3.19.7), IRanges, GenomicRanges, Rsamtools Imports: methods, utils, stats, BiocGenerics, snpStats, ff, AnnotationDbi, Biobase, bit, VariantAnnotation Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP.20120608 Enhances: MatrixEQTL License: Artistic-2.0 Package: girafe Version: 1.12.0 Depends: R (>= 2.10.0), methods, IRanges (>= 1.3.53), Rsamtools, ShortRead (>= 1.3.21), intervals (>= 0.13.1), genomeIntervals (>= 1.7.3), grid Imports: methods, Biobase, Biostrings, BSgenome, graphics, grDevices, stats, utils, IRanges Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 Archs: i386, x64 Package: GLAD Version: 2.24.0 Depends: R (>= 2.10) Suggests: aws, tcltk License: GPL-2 Archs: i386, x64 Package: GlobalAncova Version: 3.28.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi Suggests: Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db, vsn, GSEABase, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Package: globaltest Version: 5.14.0 Depends: methods Imports: Biobase, survival, AnnotationDbi, annotate, multtest, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, annotate, Biobase, survival, GSEABase, penalized, gss, MASS, boot, rpart License: GPL (>= 2) Package: GOFunction Version: 1.6.0 Depends: R (>= 2.11.0), methods, Biobase (>= 2.8.0), graph (>= 1.26.0), Rgraphviz (>= 1.26.0), GO.db (>= 2.4.1), AnnotationDbi (>= 1.10.2), SparseM (>= 0.85) Imports: methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, SparseM License: GPL (>= 2) Package: goProfiles Version: 1.22.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db License: GPL-2 Package: GOSemSim Version: 1.18.0 Depends: R (>= 2.10), Rcpp Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db LinkingTo: Rcpp Suggests: DOSE, clusterProfiler, BiocInstaller License: GPL-2 Archs: i386, x64 Package: goseq Version: 1.12.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase Imports: mgcv, graphics, stats, utils, AnnotationDbi Suggests: GO.db, edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) Package: GOstats Version: 2.26.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.3.26), graph Imports: AnnotationDbi 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License_restricts_use: yes Archs: i386, x64 Package: GraphAT Version: 1.32.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL Package: graphite Version: 1.6.0 Depends: R (>= 2.10), graph Imports: AnnotationDbi, graph, graphics, methods, org.Hs.eg.db, stats, utils Suggests: DEGraph (>= 1.4), hgu133plus2.db, RCytoscape (>= 1.6), SPIA (>= 2.2), topologyGSA (>= 1.0), clipper, ALL License: AGPL-3 Package: GraphPAC Version: 1.2.2 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 Package: GRENITS Version: 1.12.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) Archs: i386, x64 Package: GSEABase Version: 1.22.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), annotate, methods, graph (>= 1.37.2) Imports: BiocGenerics, annotate, 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GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow License: Artistic-2.0 Package: htSeqTools Version: 1.6.1 Depends: R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase, IRanges, methods, MASS, BSgenome, GenomicRanges Enhances: parallel License: GPL (>= 2) Package: HTSFilter Version: 1.0.1 Depends: methods, Biobase (>= 2.16.0), R (>= 2.10.0) Imports: DESeq (>= 1.8.3), edgeR (>= 2.6.12), DESeq2, GenomicRanges, IRanges Suggests: EDASeq (>= 1.2.0) License: Artistic-2.0 Package: HybridMTest Version: 1.4.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) Package: hyperdraw Version: 1.12.0 Depends: R (>= 2.9.0), methods, grid, graph, hypergraph, Rgraphviz Imports: stats4 License: GPL (>= 2) Package: hypergraph Version: 1.32.0 Depends: R (>= 2.1.0), methods, graph License: Artistic-2.0 Package: iASeq Version: 1.4.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 Package: iBBiG Version: 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gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE, methods Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX Enhances: doMC License: GPL-2 Package: minet Version: 3.14.0 Depends: infotheo License: CC BY-NC-SA 3.0 Archs: i386, x64 Package: minfi Version: 1.6.0 Depends: methods, BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), lattice, reshape, GenomicRanges, Biostrings, utils Imports: BiocGenerics, beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, illuminaio, matrixStats, mclust Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), minfiData (>= 0.2.0), RUnit, digest License: Artistic-2.0 Package: MinimumDistance Version: 1.4.0 Depends: R (>= 2.14), BiocGenerics (>= 0.3.2), IRanges (>= 1.13.30) Imports: methods, DNAcopy, utils, msm, lattice, BiocGenerics, VanillaICE (>= 1.21.24), ff, Biobase (>= 2.17.8), foreach, oligoClasses (>= 1.21.12), GenomicRanges, matrixStats Suggests: human610quadv1bCrlmm (>= 1.0.3), SNPchip, RUnit Enhances: snow, doSNOW License: Artistic-2.0 Package: MiPP Version: 1.32.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) Package: MiRaGE Version: 1.2.0 Depends: R (>= 2.12.1), Biobase(>= 2.16.0) Imports: AnnotationDbi, BiocGenerics Suggests: seqinr (>= 3.0.3), biomaRt (>= 2.6.0), GenomicFeatures (>= 1.8.1), Biostrings (>= 2.24.1), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, miRNATarget, humanStemCell, IRanges , GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL Package: miRNApath Version: 1.20.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 Package: MLInterfaces Version: 1.40.0 Depends: R (>= 2.9), Biobase, MASS, methods, genefilter, rpart, rda, annotate, cluster, sfsmisc Imports: mboost, gdata, pls Suggests: class, e1071, ipred, randomForest, gpls, pamr, rpart, MASS, nnet, ALL, gbm, mlbench, hgu95av2.db, som, RColorBrewer, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, gbm, mboost, sfsmisc, party Enhances: parallel License: LGPL Package: MLP Version: 1.8.1 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 Package: MMDiff Version: 1.0.0 Depends: R (>= 2.14.0),GenomicRanges,parallel,DiffBind,GMD,Rsamtools Imports: GenomicRanges,IRanges Suggests: MMDiffBamSubset License: Artistic-2.0 Package: MmPalateMiRNA Version: 1.10.0 Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod, lattice, vsn Imports: limma, lattice, Biobase Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra License: GPL-3 Package: mosaics Version: 1.8.0 Depends: R (>= 2.11.1), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) Archs: i386, x64 Package: MotifDb Version: 1.2.2 Depends: R (>= 2.15.0), methods, IRanges, Biostrings Imports: BiocGenerics, rtracklayer Suggests: RUnit, MotIV, seqLogo License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes Package: motifRG Version: 1.4.0 Depends: R (>= 2.10) Imports: Biostrings, IRanges, seqLogo, parallel, methods, grid,graphics License: Artistic-2.0 Package: motifStack Version: 1.4.0 Depends: R (>= 2.15.1), methods, grImport, grid, MotIV, ade4 Imports: grImport, grid, XML, ade4 Suggests: RUnit, BiocGenerics, MotifDb, RColorBrewer License: GPL (>= 2) Package: MotIV Version: 1.16.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.0) Imports: graphics, grid, methods, BiocGenerics, IRanges (>= 1.13.5), Biostrings (>= 1.24.0), lattice, rGADEM, stats, utils Suggests: rtracklayer License: GPL-2 Archs: i386, x64 Package: MSnbase Version: 1.8.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.3), Biobase (>= 2.15.2), ggplot2, mzR Imports: plyr, IRanges, preprocessCore, vsn, grid, reshape2, stats4, affy, impute Suggests: testthat, zoo, knitr, rols, Rdisop Enhances: foreach, doMC, parallel License: Artistic-2.0 Package: Mulcom Version: 1.10.0 Depends: R (>= 2.10), fields, Biobase Imports: graphics, grDevices, stats, methods License: GPL-2 Archs: i386, x64 Package: multiscan Version: 1.20.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) Archs: i386, x64 Package: multtest Version: 2.16.0 Depends: R (>= 2.10), methods, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL Archs: i386, x64 Package: MVCClass Version: 1.34.0 Depends: R (>= 2.1.0), methods License: LGPL Package: mzR Version: 1.6.3 Depends: Rcpp (>= 0.10.1), methods, utils Imports: Biobase LinkingTo: Rcpp Suggests: msdata (>= 0.1.9), RUnit, faahKO License: Artistic-2.0 Archs: i386, x64 Package: NarrowPeaks Version: 1.4.0 Depends: R (>= 2.10.0), splines Imports: GenomicRanges, IRanges, fda, CSAR Suggests: rtracklayer, GenomicRanges, CSAR License: Artistic-2.0 Archs: i386, x64 Package: NCIgraph Version: 1.8.0 Depends: graph, R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCytoscape, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 Package: nem Version: 2.36.0 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), plotrix, limma, cluster (>= 1.11), statmod, Hmisc, Rgraphviz Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz Suggests: Biobase (>= 1.10) Enhances: doMC, Rglpk License: GPL (>= 2) Archs: i386, x64 Package: netresponse Version: 1.12.0 Depends: R (>= 2.15.1), dmt, igraph0, infotheo, ggplot2, graph, mclust, methods, minet, parallel, qvalue, RColorBrewer, reshape, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Package: networkBMA Version: 1.2.0 Depends: R (>= 2.15.0), stats, utils, BMA License: GPL (>= 2) Package: nnNorm Version: 2.24.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL Package: NOISeq Version: 2.0.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1) License: Artistic-2.0 Package: NormqPCR Version: 1.6.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR Imports: ReadqPCR License: LGPL-3 Package: NTW Version: 1.10.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 Package: nucleR Version: 1.8.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Biobase (>= 2.15.1), ShortRead, parallel Imports: methods, BiocGenerics, IRanges, Biobase, ShortRead, GenomicRanges, stats Enhances: htSeqTools License: LGPL (>= 3) Package: nudge Version: 1.26.0 Imports: stats License: GPL-2 Package: NuPoP Version: 1.10.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: occugene Version: 1.20.0 Depends: R (>= 2.0.0) License: GPL (>= 2) Package: OCplus Version: 1.34.0 Depends: R (>= 2.1.0), akima Imports: multtest (>= 1.7.3), graphics, grDevices, stats License: LGPL Package: oligo Version: 1.24.2 Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43), Biobase (>= 2.17.8) Imports: affyio (>= 1.25.0), affxparser (>= 1.29.11), Biostrings (>= 2.25.12), BiocGenerics (>= 0.3.2), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore (>= 1.19.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, RUnit Enhances: ff, doMC, doMPI License: LGPL (>= 2) Archs: i386, x64 Package: oligoClasses Version: 1.22.0 Depends: R (>= 2.14), BiocGenerics (>= 0.3.2) Imports: BiocGenerics, Biobase (>= 2.17.8), methods, graphics, IRanges (>= 1.13.30), GenomicRanges, Biostrings (>= 2.23.6), affyio (>= 1.23.2), ff, foreach, BiocInstaller, utils Suggests: RSQLite, hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), crlmm, SNPchip, VanillaICE, RUnit, human370v1cCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) Package: OLIN Version: 1.38.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 Package: OLINgui Version: 1.34.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 Package: oneChannelGUI Version: 1.26.0 Depends: Biobase, affylmGUI, tkWidgets, IRanges, Rsamtools, Biostrings, siggenes, chimera Suggests: annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno, chipseq, BSgenome, Rgraphviz, affy ,annaffy, affyPLM, multtest, ssize, sizepower, RankProd, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, edgeR, metaArray, MergeMaid, biomaRt, GenomeGraphs,AffyCompatible, rtracklayer, Genominator, EDASeq, limma, DESeq, DEXSeq, goseq, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, ragene10sttranscriptcluster.db, GOstats, AnnotationDbi, preprocessCore, baySeq, HuExExonProbesetLocation, MoExExonProbesetLocation, RaExExonProbesetLocation, snow, RmiR, RmiR.Hs.miRNA, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn4, R.utils, cummeRbund License: Artistic-2.0 Package: ontoCAT Version: 1.12.0 Depends: rJava, methods License: Apache License 2.0 Package: OrderedList Version: 1.32.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2), methods Imports: Biobase, graphics, methods, stats, twilight License: GPL (>= 2) Package: OrganismDbi Version: 1.2.0 Depends: R (>= 2.14.0), methods, AnnotationDbi (>= 1.16.10), GenomicFeatures Imports: BiocGenerics, graph, RBGL, AnnotationDbi Suggests: Homo.sapiens, Rattus.norvegicus, RUnit License: Artistic-2.0 Package: OSAT Version: 1.8.1 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 Package: OTUbase Version: 1.10.0 Depends: R (>= 2.9.0), methods, ShortRead (>= 1.4.0), Biobase, vegan Imports: Biostrings, ShortRead, IRanges License: Artistic-2.0 Package: OutlierD Version: 1.24.0 Depends: R (>= 2.3.0), Biobase, quantreg License: GPL (>= 2) Package: PADOG Version: 1.2.0 Depends: R (>= 2.14.0), KEGGdzPathwaysGEO, graphics, limma, AnnotationDbi, Biobase, methods, nlme, GSA,KEGG.db Imports: graphics, limma, hgu133plus2.db, hgu133a.db, KEGG.db, AnnotationDbi, Biobase, methods, nlme Suggests: parallel License: GPL (>= 2) Package: PAnnBuilder Version: 1.24.0 Depends: R (>= 2.7.0), methods, utils, RSQLite, Biobase (>= 1.17.0), AnnotationDbi (>= 1.3.12) Imports: methods, utils, Biobase, DBI, RSQLite, AnnotationDbi Suggests: org.Hs.ipi.db License: LGPL (>= 2.0) Package: panp Version: 1.30.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) Package: PANR Version: 1.6.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils Suggests: snow, RedeR License: Artistic-2.0 Package: PAPi Version: 1.0.0 Depends: R (>= 2.15.2), svDialogs, KEGGREST License: GPL (>= 2) Package: parody Version: 1.18.0 Depends: R (>= 2.5.0), methods, tools, utils License: Artistic-2.0 Package: PathNet Version: 1.0.0 Depends: R (>= 1.14.0) Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 Package: pathRender Version: 1.28.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods Suggests: ALL, hgu95av2.db License: LGPL Package: pathview Version: 1.1.4 Depends: R (>= 2.10), KEGGgraph, org.Hs.eg.db Imports: Rgraphviz, graph, png, AnnotationDbi, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) Package: pcaGoPromoter Version: 1.4.0 Depends: R (>= 2.14.0) , ellipse Imports: Biobase (>= 2.10.0) , AnnotationDbi Suggests: Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, Biostrings, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, serumStimulation, parallel License: GPL (>= 2) Package: pcaMethods Version: 1.50.0 Depends: Biobase, methods, Rcpp (>= 0.8.7) Imports: BiocGenerics, MASS LinkingTo: Rcpp Suggests: matrixStats, lattice License: GPL (>= 3) Archs: i386, x64 Package: pcot2 Version: 1.28.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800.db, KEGG.db, mvtnorm License: GPL (>= 2) Package: PCpheno Version: 1.22.0 Depends: R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats, ppiData, annotate (>= 1.17.4) Imports: AnnotationDbi, Biobase, Category, GO.db, graph, graphics, GSEABase, KEGG.db, methods, ScISI, stats, stats4 Suggests: KEGG.db, GO.db, org.Sc.sgd.db License: Artistic-2.0 Package: pdInfoBuilder Version: 1.24.0 Depends: R (>= 2.15.0), methods, Biobase (>= 2.17.7), RSQLite (>= 0.11.1), affxparser (>= 1.29.12), oligo (>= 1.21.5) Imports: Biostrings (>= 2.25.12), IRanges (>= 1.15.44) License: Artistic-2.0 Archs: i386, x64 Package: pdmclass Version: 1.32.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda License: Artistic-2.0 Package: PGSEA Version: 1.34.0 Depends: R (>= 2.10), GO.db, KEGG.db, AnnotationDbi, annaffy, methods, Biobase (>= 2.5.5) Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma License: GPL-2 Package: phenoDist Version: 1.8.0 Depends: R (>= 2.9.0), imageHTS, e1071 Suggests: GOstats, MASS License: LGPL-2.1 Package: phenoTest Version: 1.8.1 Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR Suggests: GSEABase, KEGG.db, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) Package: phyloseq Version: 1.4.5 Depends: R (>= 2.15.2), methods, ade4 (>= 1.4.17), picante (>= 1.5.2) Imports: ape (>= 3.0.7), Biostrings (>= 2.26.3), foreach (>= 1.4), ggplot2 (>= 0.9.3), igraph (>= 0.6.5.2), multtest (>= 2.14), plyr (>= 1.8), reshape (>= 0.8.4), RJSONIO (>= 1.0.1), scales (>= 0.2.3), vegan (>= 2.0.6) Suggests: genefilter (>= 1.40), testthat (>= 0.7) Enhances: doParallel (>= 1.0.1) License: AGPL-3 Package: piano Version: 1.0.7 Depends: R (>= 2.14.0) Imports: Biobase, gplots, igraph, relations, marray Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt License: GPL (>= 2) Package: pickgene Version: 1.32.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) Package: PICS Version: 2.4.1 Depends: R (>= 2.14.0), BiocGenerics (>= 0.1.3) Imports: methods, stats4, IRanges, GenomicRanges, graphics, grDevices, stats, Rsamtools Suggests: ShortRead, rtracklayer, parallel License: Artistic-2.0 Archs: i386, x64 Package: PING Version: 2.4.0 Depends: R(>= 2.15.0), chipseq, IRanges, GenomicRanges Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 Archs: i386, x64 Package: pint Version: 1.12.0 Depends: mvtnorm, methods, graphics, Matrix, dmt License: FreeBSD Package: pkgDepTools Version: 1.26.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl, BiocInstaller License: GPL-2 Package: plateCore Version: 1.18.0 Depends: R (>= 2.10), flowCore, flowViz, lattice, latticeExtra Imports: Biobase, flowCore, graphics, grDevices, lattice, MASS, methods, robustbase, stats, utils Suggests: gplots License: Artistic-2.0 Package: plgem Version: 1.32.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), MASS Imports: utils License: GPL-2 Package: plier Version: 1.30.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) Archs: i386, x64 Package: PLPE Version: 1.20.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) Package: plrs Version: 1.0.0 Depends: R (>= 2.10), Biobase Imports: BiocGenerics, CGHbase, graphics, grDevices, ic.infer, marray, methods, quadprog, Rcsdp, stats, stats4, utils Suggests: mvtnorm, methods License: GPL (>= 2.0) Package: plw Version: 1.20.0 Depends: R (>= 2.10), affy (>= 1.23.4) Imports: MASS, affy, graphics, splines, stats Suggests: limma License: GPL-2 Archs: i386, x64 Package: ppiStats Version: 1.26.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.19) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable License: Artistic-2.0 Package: prada Version: 1.36.1 Depends: R (>= 2.10.0), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, BiocGenerics, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, stats4, utils Suggests: cellHTS, tcltk License: LGPL Archs: i386, x64 Package: prebs Version: 1.0.2 Depends: R (>= 2.14.0), Rsamtools, affy Imports: parallel, methods, stats, GenomicRanges, IRanges Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 Package: PREDA Version: 1.6.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, samr, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 Package: preprocessCore Version: 1.22.0 Depends: methods Imports: stats License: LGPL (>= 2) Archs: i386, x64 Package: PROcess Version: 1.36.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 Package: procoil Version: 1.10.0 Depends: R (>= 2.10.1), methods Imports: methods, stats, graphics, utils Suggests: Biostrings License: GPL (>= 2) Package: pRoloc Version: 1.0.1 Depends: R (>= 2.15), MSnbase (>= 1.7.23), MLInterfaces (>= 1.37.1), methods Imports: mclust, MSBVAR, caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, BiocGenerics, stats4, RColorBrewer, scales, MASS, knitr Suggests: testthat, pRolocdata, roxygen2 License: GPL-2 Package: PROMISE Version: 1.12.0 Depends: R (>= 2.11.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) Package: proteinProfiles Version: 1.0.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 Package: puma Version: 3.2.1 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.23.4), graphics, grDevices, methods, stats, utils, mclust Imports: Biobase (>= 2.5.5), affy (>= 1.23.4),affyio Suggests: pumadata, affydata, snow, limma, annotate, ROCR License: LGPL Archs: i386, x64 Package: pvac Version: 1.8.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) Package: pvca Version: 1.0.1 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, lme4 Suggests: golubEsets License: LGPL (>= 2.0) Package: PWMEnrich Version: 2.2.0 Depends: methods, grid, BiocGenerics, Biostrings, Imports: seqLogo, gdata, evd Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel License: GPL-3 Package: qpcrNorm Version: 1.18.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) Package: qpgraph Version: 1.16.3 Depends: R (>= 2.14.0) Imports: methods, Matrix (>= 1.0), graphics, annotate, graph (>= 1.37.6), Biobase, GGBase, AnnotationDbi, mvtnorm, qtl, Rgraphviz Suggests: genefilter, org.EcK12.eg.db Enhances: rlecuyer, snow, Category, GOstats License: GPL (>= 2) Archs: i386, x64 Package: qrqc Version: 1.14.0 Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable, Rsamtools (>= 1.3.28), testthat Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats LinkingTo: Rsamtools License: GPL (>= 2) Archs: i386, x64 Package: quantsmooth Version: 1.26.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 Package: QuasR Version: 1.0.9 Depends: R (>= 2.15.0), parallel, GenomicRanges, Rbowtie (>= 0.99.0) Imports: methods, zlibbioc, BiocGenerics, IRanges, BiocInstaller, Biobase, Biostrings, GenomicRanges, BSgenome, Rsamtools, GenomicFeatures, ShortRead LinkingTo: Rsamtools Suggests: Rsamtools, rtracklayer, Gviz, RUnit License: GPL-2 Archs: i386, x64 Package: qvalue Version: 1.34.0 Imports: graphics, grDevices, stats, tcltk License: LGPL Package: r3Cseq Version: 1.6.0 Depends: GenomicRanges,Rsamtools,data.table,rtracklayer,VGAM,qvalue,RColorBrewer,sqldf,methods Suggests: BSgenome.Mmusculus.UCSC.mm9,BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 Package: R453Plus1Toolbox Version: 1.10.0 Depends: R (>= 2.12.0), BiocGenerics, Biobase, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer2,TeachingDemos Imports: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), biomaRt, Biostrings, BSgenome, IRanges (>= 1.17.24), methods, R2HTML, Rsamtools, rtracklayer, ShortRead, VariantAnnotation, xtable, tools Suggests: rtracklayer, ShortRead, Rsamtools, BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Archs: i386, x64 Package: rama Version: 1.34.0 Depends: R(>= 2.5.0) License: GPL (>= 2) Archs: i386, x64 Package: RamiGO Version: 1.6.0 Depends: gsubfn,methods Imports: igraph,RCurl,png,RCytoscape,graph License: Artistic-2.0 Package: randPack Version: 1.6.0 Depends: methods Imports: Biobase License: Artistic-2.0 Package: RankProd Version: 2.32.0 Depends: R (>= 1.9.0) Imports: graphics License: file LICENSE License_restricts_use: yes Package: RbcBook1 Version: 1.28.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 Package: RBGL Version: 1.36.2 Depends: graph, methods Imports: methods Suggests: Rgraphviz, XML License: Artistic-2.0 Archs: i386, x64 Package: RBioinf Version: 1.20.0 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Package: rBiopaxParser Version: 1.0.0 Imports: XML Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics License: GPL (>= 2) Package: Rbowtie Version: 1.0.3 Suggests: parallel License: Artistic-1.0 | file LICENSE Package: rbsurv Version: 2.18.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) Package: Rcade Version: 1.2.0 Depends: R (>= 2.14.0), methods, GenomicRanges, baySeq, Rsamtools Imports: graphics, IRanges, rgl Suggests: limma, biomaRt, RUnit, BiocGenerics License: GPL-2 Package: RCASPAR Version: 1.6.0 License: GPL (>= 3) Package: RchyOptimyx Version: 1.4.0 Depends: R (>= 2.10), Rgraphviz (>= 2.2.1) Imports: Rgraphviz, sfsmisc, graphics, methods, graph, grDevices Suggests: flowCore, flowType License: Artistic-2.0 Archs: i386, x64 Package: RCytoscape Version: 1.10.0 Depends: R (>= 2.14.0), graph (>= 1.31.0), XMLRPC (>= 0.2.4) Imports: methods, XMLRPC, BiocGenerics Suggests: RUnit License: GPL-2 Package: Rdisop Version: 1.20.0 Depends: R (>= 2.0.0), RcppClassic, Rcpp LinkingTo: RcppClassic, Rcpp Suggests: RUnit License: GPL-2 Archs: i386, x64 Package: RDRToolbox Version: 1.10.0 Depends: R (>= 2.9.0),rgl Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) Package: ReactomePA Version: 1.4.0 Depends: R (>= 2.10), DOSE Imports: methods, AnnotationDbi, reactome.db, org.Hs.eg.db, stats4, plyr, igraph, qvalue, graphics Suggests: clusterProfiler, GOSemSim, org.Hs.eg.db License: GPL-2 Package: ReadqPCR Version: 1.6.0 Depends: R(>= 2.14.0), Biobase, methods, affy Imports: Biobase Suggests: qpcR License: LGPL-3 Package: reb Version: 1.38.0 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) License: GPL-2 Archs: i386, x64 Package: RedeR Version: 1.8.3 Depends: R (>= 2.15), methods, igraph Imports: RCurl, XML, XMLRPC, rJava Suggests: JavaGD, PANR, pvclust License: GPL (>= 2) Package: REDseq Version: 1.6.0 Depends: R (>= 2.15.0), BiocGenerics (>= 0.1.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges (>= 1.13.5), multtest, stats, utils License: GPL (>= 2) Package: RefPlus Version: 1.30.0 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) Package: Repitools Version: 1.6.0 Depends: R (>= 2.13.0), methods, BiocGenerics (>= 0.1.0), GenomicRanges (>= 1.7.8) Imports: BiocGenerics, IRanges (>= 1.13.5), GenomicRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR (>= 2.99.2), DNAcopy, Ringo, aroma.affymetrix, Rsolnp, snowfall, parallel Suggests: GenomicRanges, IRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, ShortRead, BSgenome.Hsapiens.UCSC.hg18, rtracklayer License: LGPL (>= 2) Archs: i386, x64 Package: ReportingTools Version: 2.0.1 Depends: methods Imports: Biobase,hwriter,Category,GOstats,limma,lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, ggplot2, ggbio Suggests: RUnit, ggplot2, ggbio, ALL, hgu95av2.db, org.Mm.eg.db, knitr License: Artistic-2.0 Package: ReQON Version: 1.6.0 Depends: R (>= 2.15.0), Rsamtools, seqbias Imports: rJava, graphics, stats, utils, grDevices License: GPL-2 Package: Resourcerer Version: 1.34.0 Depends: R (>= 1.9.0), Biobase, AnnotationDbi (>= 1.4.0) Suggests: human.db0, mouse.db0, rat.db0 License: LGPL Package: rGADEM Version: 2.8.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, IRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 Archs: i386, x64 Package: RGalaxy Version: 1.4.0 Depends: XML, methods, tools, optparse, digest, Imports: BiocGenerics, Biobase, roxygen2 Suggests: RUnit, hgu95av2.db, knitr, formatR, Rserve Enhances: RSclient License: Artistic-2.0 Package: Rgraphviz Version: 2.4.1 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graph, graphics, grDevices, grid, methods, utils Suggests: RUnit, BiocGenerics, XML License: file LICENSE Archs: i386, x64 Package: rhdf5 Version: 2.4.0 Depends: methods Imports: zlibbioc Suggests: bit64 License: Artistic-2.0 Archs: i386, x64 Package: rHVDM Version: 1.26.0 Depends: R (>= 2.10), R2HTML (>= 1.5), affy (>= 1.23.4), minpack.lm (>= 1.0-5), Biobase (>= 2.5.5) License: GPL-2 Package: Ringo Version: 1.24.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4 Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 Archs: i386, x64 Package: RIPSeeker Version: 1.0.0 Depends: R (>= 2.15), methods, IRanges, GenomicRanges, rtracklayer, Rsamtools Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures License: GPL-2 Package: Risa Version: 1.2.2 Depends: R (>= 2.0.9), Biobase (>= 2.4.0), methods, Rcpp (>= 0.9.13), biocViews, affy Imports: xcms Suggests: faahKO (>= 1.2.11) License: LGPL Package: RLMM Version: 1.22.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) Package: Rmagpie Version: 1.16.0 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) Package: RMAPPER Version: 1.10.0 Depends: methods Suggests: RCurl License: Artistic-2.0 Package: RMassBank Version: 1.2.1 Depends: rcdk,yaml,mzR,methods,rjson Imports: XML,RCurl Suggests: gplots,RMassBankData,xcms License: Artistic-2.0 Package: RmiR Version: 1.16.0 Depends: R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice Imports: DBI, methods, stats Suggests: hgug4112a.db,org.Hs.eg.db License: Artistic-2.0 Package: RNAinteract Version: 1.8.0 Depends: R (>= 2.12.0), abind, locfit, Biobase Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12) License: Artistic-2.0 Package: RNAither Version: 2.8.0 Depends: R (>= 2.10), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt, car, splots, methods License: Artistic-2.0 Package: RNASeqPower Version: 1.0.0 License: LGPL (>= 2) Package: ROC Version: 1.36.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase License: Artistic-2.0 Archs: i386, x64 Package: Rolexa Version: 1.16.0 Depends: R (>= 2.9.0), graphics, grDevices, methods, ShortRead Imports: mclust, Biostrings, graphics, grDevices, IRanges, methods, ShortRead, stats Enhances: fork License: GPL-2 Package: rols Version: 1.2.2 Depends: methods Imports: XML, XMLSchema (>= 0.6.0), SSOAP (>= 0.8.0), Biobase Suggests: xtable, GO.db, knitr (>= 1.1.0) License: GPL-2 Package: ROntoTools Version: 1.0.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) Package: RPA Version: 1.16.0 Depends: R (>= 2.15.0), affy, affydata, methods, parallel License: FreeBSD Package: RpsiXML Version: 2.2.0 Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL 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graph, utils License: Artistic-2.0 Archs: i386, x64 Package: RSVSim Version: 1.0.2 Depends: R (>= 3.0.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, MASS, rtracklayer License: LGPL-3 Package: rTANDEM Version: 1.0.1 Depends: XML, Rcpp, data.table (>= 1.8.8) Imports: methods LinkingTo: Rcpp Suggests: biomaRt License: Artistic-1.0 | file LICENSE Archs: i386, x64 Package: RTCA Version: 1.12.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 Package: RTopper Version: 1.6.0 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db License: GPL (>= 3) Package: rtracklayer Version: 1.20.4 Depends: R (>= 2.10), methods, GenomicRanges (>= 1.11.12) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.1.0), IRanges (>= 1.15.37), GenomicRanges, Biostrings (>= 2.25.6), BSgenome (>= 1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.7.3) LinkingTo: IRanges Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db License: Artistic-2.0 Archs: i386, x64 Package: Rtreemix Version: 1.22.0 Depends: R (>= 2.5.0), methods, graph, Biobase Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL Archs: i386, x64 Package: safe Version: 3.0.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, KEGG.db, PFAM.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) Package: sagenhaft Version: 1.30.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, methods, SparseM, stats, utils License: GPL (>= 2) Package: SAGx Version: 1.34.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase, stats4 Suggests: KEGG.db, hu6800.db, MASS License: GPL-3 Archs: i386, x64 Package: SamSPECTRAL Version: 1.14.1 Depends: R (>= 2.10) Imports: methods License: GPL (>= 2) Archs: i386, x64 Package: SANTA Version: 1.0.0 Depends: R (>= 2.14), igraph, snow Imports: msm Suggests: RUnit, BiocGenerics, org.Sc.sgd.db License: Artistic-2.0 Archs: i386, x64 Package: SBMLR Version: 1.56.0 Depends: XML, deSolve License: GPL-2 Package: SCAN.UPC Version: 2.0.2 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings Imports: utils, methods, MASS, tools Suggests: pd.hg.u95a License: MIT Package: ScISI Version: 1.32.0 Depends: R (>= 2.10), GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable License: LGPL Package: segmentSeq Version: 1.12.1 Depends: R (>= 2.3.0), methods, baySeq (>= 1.11.1), ShortRead, GenomicRanges, IRanges Imports: baySeq, graphics, grDevices, IRanges, methods, utils, GenomicRanges Suggests: snow License: GPL-3 Package: SeqArray Version: 1.0.0 Depends: gdsfmt (>= 0.9.12) Suggests: parallel, snow License: GPL-3 Archs: i386, x64 Package: seqbias 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MASS, mvtnorm, quadprog, penalized (>= 0.9-39), snowfall, stats License: GPL (>= 2) Package: siggenes Version: 1.34.0 Depends: methods, Biobase, multtest, splines, graphics Imports: stats4 Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5) License: LGPL (>= 2) Package: sigPathway Version: 1.28.0 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 Archs: i386, x64 Package: SIM Version: 1.30.0 Depends: R (>= 2.4), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) Archs: i386, x64 Package: simpleaffy Version: 2.36.1 Depends: R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6), genefilter, gcrma Imports: methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma License: GPL (>= 2) Archs: i386, x64 Package: sizepower Version: 1.30.0 Depends: stats License: LGPL 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GPL-2 Package: SPIA Version: 2.12.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: GPL (>= 2) Package: spikeLI Version: 2.20.0 Imports: graphics, grDevices, stats, utils License: GPL-2 Package: spkTools Version: 1.16.0 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) Package: splicegear Version: 1.32.0 Depends: R (>= 2.6.0), methods, Biobase(>= 2.5.5) Imports: annotate, Biobase, graphics, grDevices, grid, methods, utils, XML License: LGPL Package: SplicingGraphs Version: 1.0.4 Depends: BiocGenerics, IRanges (>= 1.17.43), GenomicRanges (>= 1.11.45), GenomicFeatures, Rgraphviz (>= 2.3.7) Imports: methods, utils, igraph, BiocGenerics, IRanges, GenomicRanges, GenomicFeatures, graph, Rgraphviz Suggests: igraph, Gviz, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 Package: splots Version: 1.26.0 Imports: grid, RColorBrewer License: LGPL Package: spotSegmentation Version: 1.34.0 Depends: R (>= 2.10), mclust License: GPL (>= 2) Package: SQUADD Version: 1.10.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>= 2) Package: SRAdb Version: 1.14.0 Depends: RSQLite (>= 0.8-4) , graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 Package: sscore Version: 1.32.0 Depends: R (>= 1.8.0), affy, affyio Suggests: affydata License: GPL (>= 2) Package: ssize Version: 1.34.0 Depends: gdata, xtable License: LGPL Package: SSPA Version: 2.0.3 Depends: R (>= 2.12), methods, qvalue, lattice, limma Imports: graphics, stats Suggests: genefilter, edgeR, DESeq License: GPL (>= 2) Archs: i386, x64 Package: staRank Version: 1.2.0 Depends: methods, cellHTS2, R (>= 2.10) License: GPL Package: Starr Version: 1.16.0 Depends: Ringo, affy, affxparser Imports: pspline, MASS, zlibbioc License: Artistic-2.0 Archs: i386, x64 Package: stepNorm Version: 1.32.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL Package: stepwiseCM Version: 1.6.0 Depends: R (>= 2.14), randomForest, MAclinical, tspair, pamr, snowfall, glmpath, penalized, e1071 License: GPL Package: Streamer Version: 1.6.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), Rgraphviz License: Artistic-2.0 Archs: i386, x64 Package: survcomp Version: 1.10.0 Depends: R (>= 2.10), survival, prodlim Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta Suggests: Hmisc, CPE, clinfun, survJamda, Biobase, xtable License: Artistic-2.0 Archs: i386, x64 Package: sva Version: 3.6.0 Depends: R (>= 2.8), corpcor, mgcv Imports: graphics, stats Suggests: limma,pamr,bladderbatch License: Artistic-2.0 Archs: i386, x64 Package: synapter Version: 1.2.0 Depends: R (>= 2.15), methods, MSnbase Imports: hwriter, tcltk, tcltk2, RColorBrewer, lattice, qvalue, multtest, utils, Biobase, knitr Suggests: synapterdata, xtable License: GPL-2 Package: TargetSearch Version: 1.16.0 Depends: R (>= 2.7.0), mzR, methods Imports: graphics, grDevices, methods, stats, tcltk, utils Suggests: TargetSearchData License: GPL (>= 2) Archs: i386, x64 Package: TDARACNE Version: 1.10.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 Package: TEQC Version: 2.9.2 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) Package: ternarynet Version: 1.4.0 Depends: R (>= 2.10.0), methods Imports: utils, igraph License: GPL (>= 2) Archs: i386, x64 Package: tigre Version: 1.14.1 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, BiocGenerics, Biobase, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite Suggests: puma, drosgenome1.db, annotate, lumi License: AGPL-3 Archs: i386, x64 Package: tilingArray Version: 1.38.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 Archs: i386, x64 Package: timecourse Version: 1.32.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL Package: tkWidgets Version: 1.38.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 Package: topGO Version: 2.12.0 Depends: R (>= 2.10.0), methods, graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: methods, graph, Biobase, SparseM, AnnotationDbi, lattice Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL Package: TransView Version: 1.4.5 Depends: methods,GenomicRanges Imports: Rsamtools,zlibbioc,gplots,IRanges LinkingTo: Rsamtools Suggests: RUnit,pasillaBamSubset License: GPL-3 Archs: i386, x64 Package: triform Version: 1.2.0 Depends: R (>= 2.11.0), IRanges, yaml Imports: IRanges, yaml, BiocGenerics Suggests: RUnit License: GPL-2 Package: trigger Version: 1.6.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 Archs: i386, x64 Package: triplex Version: 1.0.10 Depends: R (>= 2.15.0), Biostrings (>= 2.26.0) Imports: methods, grid, Biostrings, GenomicRanges LinkingTo: Biostrings, IRanges Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs License: BSD Archs: i386, x64 Package: tspair Version: 1.18.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 Archs: i386, x64 Package: TSSi Version: 1.6.0 Depends: R (>= 2.13.2), BiocGenerics (>= 0.3.2) Imports: BiocGenerics, methods, Hmisc, minqa, stats, Biobase (>= 0.3.2), plyr, IRanges Suggests: rtracklayer Enhances: multicore License: GPL-3 Archs: i386, x64 Package: TurboNorm Version: 1.8.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: affydata, affy, lattice License: LGPL Archs: i386, x64 Package: tweeDEseq Version: 1.6.2 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) Archs: i386, x64 Package: twilight Version: 1.36.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) Archs: i386, x64 Package: TypeInfo Version: 1.26.0 Depends: methods Suggests: Biobase License: BSD Package: UniProt.ws Version: 2.0.1 Depends: RSQLite, RCurl, methods, utils Imports: BiocGenerics, AnnotationDbi Suggests: RUnit License: Artistic License 2.0 Package: VanillaICE Version: 1.22.0 Depends: R (>= 2.14.0) Imports: stats, utils, methods, Biobase, oligoClasses (>= 1.21.12),lattice, IRanges (>= 1.13.22), grid, msm, iterators, foreach, GenomicRanges, matrixStats Suggests: genomewidesnp6Crlmm (>= 1.0.7), hapmapsnp6, RColorBrewer, genefilter, RSQLite, foreach, RUnit, pd.mapping50k.hind240, SNPchip (>= 2.5.7), doSNOW Enhances: DNAcopy, crlmm (>= 1.17.14) License: LGPL-2 Archs: i386, x64 Package: VariantAnnotation Version: 1.6.8 Depends: R (>= 2.8.0), methods, BiocGenerics, GenomicRanges (>= 1.11.29), Rsamtools (>= 1.11.26), IRanges (>= 1.17.4) Imports: methods, BiocGenerics, IRanges, Biostrings, Biobase, Rsamtools, AnnotationDbi (>= 1.17.11), zlibbioc, BSgenome, GenomicFeatures (>= 1.9.35), DBI, utils LinkingTo: IRanges, Biostrings, Rsamtools Suggests: RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2 License: Artistic-2.0 Archs: i386, x64 Package: vbmp Version: 1.28.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) Package: Vega Version: 1.8.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: VegaMC Version: 2.7.0 Depends: R (>= 2.10.0), biomaRt, Biobase, genoset Imports: methods License: GPL-2 Archs: i386, x64 Package: virtualArray Version: 1.4.1 Depends: R (>= 2.15.0), BiocGenerics, methods, plyr, preprocessCore Imports: affy, affyPLM, AnnotationDbi, Biobase, gcrma, GEOquery, graphics, methods, reshape2, stats, utils, tseries, outliers Suggests: affydata, plier, limma, lumi, org.Hs.eg.db Enhances: multicore,BiocParallel License: GPL-3 Package: vsn Version: 3.28.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: methods, affy (>= 1.23.4), limma, lattice Suggests: affydata, hgu95av2cdf License: Artistic-2.0 Archs: i386, x64 Package: wateRmelon Version: 1.0.3 Depends: R (>= 2.10), limma, methods, matrixStats, methylumi, lumi, IlluminaHumanMethylation450k.db, ROC Suggests: RPMM Enhances: minfi, methylumi, IMA License: GPL-3 Package: waveTiling Version: 1.2.0 Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, IRanges Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart12 License: GPL (>= 2) Archs: i386, x64 Package: weaver Version: 1.26.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 Package: webbioc Version: 1.32.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocInstaller License: GPL (>= 2) Package: widgetTools Version: 1.38.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL Package: xcms Version: 1.36.0 Depends: R (>= 2.14.0), methods, mzR (>= 1.1.6), BiocGenerics, Biobase Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>= 1.5.2), RANN, RUnit Enhances: Rgraphviz, KEGGSOAP, Rmpi License: GPL (>= 2) Archs: i386, x64 Package: XDE Version: 2.6.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), methods, graphics Imports: Biobase, BiocGenerics, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils, mvtnorm Suggests: siggenes, genefilter, MASS, RColorBrewer, GeneMeta, RUnit Enhances: coda License: LGPL-2 Archs: i386, x64 Package: xmapbridge Version: 1.18.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 Package: xps Version: 1.20.3 Depends: R (>= 2.6.0), methods, utils Suggests: tools License: GPL (>= 2.0) Archs: i386 Package: yaqcaffy Version: 1.20.0 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 Package: zlibbioc Version: 1.6.0 License: Artistic-2.0 + file LICENSE Archs: i386, x64