Package: a4 Version: 1.4.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL License: GPL-3 Package: a4Base Version: 1.4.1 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL Enhances: gridSVG, JavaGD License: GPL-3 Package: a4Classif Version: 1.4.0 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL License: GPL-3 Package: a4Core Version: 1.4.0 Depends: methods, Biobase, glmnet License: GPL-3 Package: a4Preproc Version: 1.4.0 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 Package: a4Reporting Version: 1.4.0 Depends: methods, annaffy Imports: xtable, utils License: GPL-3 Package: ABarray Version: 1.24.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL Package: aCGH Version: 1.34.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, cluster, grDevices, graphics, methods, multtest, stats, survival, splines, utils License: GPL-2 Archs: i386, x64 Package: ACME Version: 2.12.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods Imports: graphics, stats License: GPL (>= 2) Archs: i386, x64 Package: ADaCGH2 Version: 1.6.0 Depends: R (>= 2.11.0), tilingArray, aCGH, waveslim, cluster, snapCGH, snowfall, ff Suggests: GLAD, DNAcopy, CGHregions, rlecuyer Enhances: Rmpi, multicore License: GPL (>= 3) Archs: i386, x64 Package: adSplit Version: 1.26.0 Depends: R (>= 2.1.0), methods (>= 2.1.0) Imports: AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db (>= 1.8.1), graphics, grDevices, KEGG.db (>= 1.8.1), methods, multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) Archs: i386, x64 Package: affxparser Version: 1.28.1 Depends: R (>= 2.6.0) Suggests: R.utils (>= 1.9.11), AffymetrixDataTestFiles License: LGPL (>= 2) Archs: i386, x64 Package: affy Version: 1.34.0 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: BiocGenerics, Biobase, affyio (>= 1.13.3), BiocInstaller, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools License: LGPL (>= 2.0) Archs: i386, x64 Package: affycomp Version: 1.32.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) Package: AffyCompatible Version: 1.16.0 Depends: R (>= 2.7.0), XML (>= 2.8-1), RCurl (>= 0.8-1), methods Imports: Biostrings License: Artistic-2.0 Package: affyContam Version: 1.14.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata License: Artistic-2.0 Package: affycoretools Version: 1.28.0 Depends: affy, Biobase, GO.db, KEGG.db Imports: biomaRt, limma, GOstats, annotate, annaffy, genefilter, gcrma, splines, xtable, AnnotationDbi, lattice Suggests: affydata, hgfocuscdf, rgl License: Artistic-2.0 Package: AffyExpress Version: 1.22.0 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: 1.8.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, methods, Biobase Suggests: AffymetrixDataTestFiles License: GPL-3 Package: affyio Version: 1.24.0 Depends: R (>= 2.6.0), methods Imports: zlibbioc License: LGPL (>= 2) Archs: i386, x64 Package: affylmGUI Version: 1.30.0 Depends: limma, tcltk, affy, Biobase, affyio Suggests: tkrplot, affyPLM, R2HTML, xtable License: LGPL Package: affyPara Version: 1.16.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0), aplpack (>= 1.1.1) Suggests: affydata Enhances: affy License: GPL-3 Package: affypdnn Version: 1.30.0 Depends: R (>= 2.13.0), affy (>= 1.5) Suggests: affydata, hgu95av2probe License: LGPL Package: affyPLM Version: 1.32.0 Depends: R (>= 2.6.0), affy (>= 1.11.0), Biobase, gcrma, stats, preprocessCore (>= 1.5.1) Imports: zlibbioc, methods LinkingTo: preprocessCore Suggests: affydata, MASS License: GPL (>= 2) Archs: i386, x64 Package: affyQCReport Version: 1.34.0 Depends: Biobase (>= 1.13.16), affy, lattice Imports: affy, affyPLM, Biobase, genefilter, graphics, grDevices, lattice, RColorBrewer, simpleaffy, stats, utils, xtable Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1) License: LGPL (>= 2) Package: AffyRNADegradation Version: 1.0.0 Depends: R (>= 2.9.0), methods, affy Suggests: AmpAffyExample License: GPL-2 Package: AffyTiling Version: 1.14.0 Depends: R (>= 2.6) Imports: affxparser, affy (>= 1.16), stats, utils, preprocessCore License: GPL (>= 2) Archs: i386, x64 Package: AGDEX Version: 1.4.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL (>= 2) Package: Agi4x44PreProcess Version: 1.16.0 Depends: R (>= 2.10), Biobase, limma, annotate, genefilter Suggests: vsn, affycoretools, hgug4112a.db, GO.db, marray, gplots, gtools, gdata License: GPL-3 Package: AgiMicroRna Version: 2.6.0 Depends: R (>= 2.10),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 Package: altcdfenvs Version: 2.18.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) Package: annaffy Version: 1.28.0 Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db Imports: AnnotationDbi (>= 0.1.15) Suggests: hgu95av2.db, multtest, tcltk License: LGPL Package: annotate Version: 1.34.1 Depends: R (>= 2.10), AnnotationDbi (>= 0.1.15) Imports: Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats, methods, XML (>= 0.92-2) Suggests: Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.4.4), rae230a.db, rae230aprobe, tkWidgets, XML (>= 0.92-2), GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz License: Artistic-2.0 Package: AnnotationDbi Version: 1.18.4 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.1.13), Biobase (>= 1.17.0) Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase, IRanges Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, human.db0, hgu95av2cdf, org.Sc.sgd.db, org.At.tair.db, affy, KEGG.db, XML, RCurl, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db License: Artistic-2.0 Package: AnnotationFuncs Version: 1.6.0 Depends: R (>= 2.7.0), AnnotationDbi Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db License: GPL-2 Package: annotationTools Version: 1.30.0 Imports: Biobase, stats License: GPL Package: anota Version: 1.4.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 Package: apComplex Version: 2.22.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL Package: aroma.light Version: 1.24.0 Depends: R.methodsS3 (>= 1.2.1) Suggests: R.oo (>= 1.8.2), R.utils (>= 1.8.2), princurve (>= 1.1-10) License: LGPL (>= 2.1) Package: ArrayExpress Version: 1.16.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, affy, limma License: Artistic-2.0 Package: arrayMvout Version: 1.14.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy, lumi Imports: simpleaffy, mdqc, affyContam, Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 Package: arrayQuality Version: 1.34.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL Package: arrayQualityMetrics Version: 3.12.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, Cairo (>= 1.4-6), genefilter, graphics, grDevices, grid, Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, simpleaffy, stats, SVGAnnotation (>= 0.9-0), utils, vsn (>= 3.23.3), XML Suggests: ALLMLL, CCl4 License: LGPL (>= 2) Package: ArrayTools Version: 1.16.0 Depends: R (>= 2.7.0), affy (>= 1.23.4), Biobase (>= 2.5.5), methods Imports: affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db License: LGPL (>= 2.0) Package: ASEB Version: 1.0.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) Archs: i386, x64 Package: attract Version: 1.8.0 Depends: R (>= 2.10.0), AnnotationDbi, KEGG.db, limma, cluster, GOstats, graphics, methods, stats Imports: Biobase, AnnotationDbi, KEGG.db, limma, cluster, GOstats, graphics, methods, stats Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) Package: BAC Version: 1.16.0 Depends: R (>= 2.10) License: Artistic-2.0 Archs: i386, x64 Package: BayesPeak Version: 1.8.0 Depends: R (>= 2.10), IRanges Imports: IRanges, graphics Enhances: multicore, snow License: GPL (>= 2) Archs: i386, x64 Package: baySeq Version: 1.10.0 Depends: R (>= 2.3.0), methods Suggests: snow, edgeR License: GPL-3 Package: BCRANK Version: 1.18.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 Archs: i386, x64 Package: beadarray Version: 2.6.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, ggplot2 Imports: BeadDataPackR, limma, AnnotationDbi, stats4, BiocGenerics, reshape2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db License: GPL-2 Archs: i386, x64 Package: beadarraySNP Version: 1.22.0 Depends: methods, Biobase (>= 2.5.5), quantsmooth Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy License: GPL-2 Package: BeadDataPackR Version: 1.8.0 License: GPL-2 Archs: i386, x64 Package: betr Version: 1.12.0 Depends: R(>= 2.6.0) Imports: Biobase (>= 2.5.5), limma, mvtnorm, methods, stats Suggests: Biobase License: LGPL Package: bgafun Version: 1.18.0 Depends: made4, seqinr,ade4 License: Artistic-2.0 Package: bgx Version: 1.20.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Suggests: affydata, hgu95av2cdf License: GPL-2 Archs: i386, x64 Package: BHC Version: 1.8.0 License: GPL-3 Archs: i386, x64 Package: BicARE Version: 1.14.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase License: GPL-2 Archs: i386, x64 Package: Biobase Version: 2.16.0 Depends: R (>= 2.10), utils, BiocGenerics (>= 0.1.0) Imports: methods, BiocGenerics Suggests: tools, tkWidgets, ALL License: Artistic-2.0 Archs: i386, x64 Package: BiocCaseStudies Version: 1.18.0 Depends: tools, methods, utils, Biobase Suggests: affy (>= 1.17.3), affyPLM (>= 1.15.1), affyQCReport (>= 1.17.0), ALL (>= 1.4.3), annaffy (>= 1.11.1), annotate (>= 1.17.3), AnnotationDbi (>= 1.1.6), apComplex (>= 2.5.0), Biobase (>= 1.17.5), bioDist (>= 1.11.3), biocGraph (>= 1.1.1), biomaRt (>= 1.13.5), CCl4 (>= 1.0.6), CLL (>= 1.2.4), Category (>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert (>= 1.15.0), gcrma (>= 2.11.1), genefilter (>= 1.17.6), geneplotter (>= 1.17.2), GO.db (>= 2.0.2), GOstats (>= 2.5.0), graph (>= 1.17.4), GSEABase (>= 1.1.13), hgu133a.db (>= 2.0.2), hgu95av2.db, hgu95av2cdf (>= 2.0.0), hgu95av2probe (>= 2.0.0), hopach (>= 1.13.0), KEGG.db (>= 2.0.2), kohonen (>= 2.0.2), lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma (>= 2.13.1), MASS (>= 7.2-38), MLInterfaces (>= 1.13.17), multtest (>= 1.19.0), org.Hs.eg.db (>= 2.0.2), ppiStats (>= 1.5.4), randomForest (>= 4.5-20), RBGL (>= 1.15.6), RColorBrewer (>= 1.0-2), Rgraphviz (>= 1.17.11), vsn (>= 3.4.0), weaver (>= 1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11) License: Artistic-2.0 Package: BiocGenerics Version: 0.2.0 Depends: methods, graphics, stats Imports: methods, graphics, stats Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, RUnit License: Artistic-2.0 Package: biocGraph Version: 1.18.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 Package: BiocInstaller Version: 1.4.9 Depends: R (>= 2.15.0) Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: biocViews Version: 1.24.0 Depends: R (>= 2.4.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl Suggests: Biobase License: Artistic-2.0 Package: bioDist Version: 1.28.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 Package: biomaRt Version: 2.12.0 Depends: methods Imports: utils, XML, RCurl Suggests: annotate License: Artistic-2.0 Package: BioMVCClass Version: 1.24.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL Package: BioNet Version: 1.14.3 Depends: R (>= 2.10.0), Biobase, graph, RBGL Imports: igraph0, AnnotationDbi Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) Package: BioSeqClass Version: 1.14.0 Depends: R (>= 2.10), scatterplot3d Imports: Biostrings, ipred, e1071, klaR, randomForest, class, tree, nnet, rpart, party, foreign, Biobase, utils, stats, grDevices Suggests: scatterplot3d License: LGPL (>= 2.0) Package: Biostrings Version: 2.24.1 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>= 1.13.6) Imports: graphics, methods, stats, utils, BiocGenerics, IRanges LinkingTo: IRanges Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy, affydata (>= 1.11.5), RUnit Enhances: Rmpi License: Artistic-2.0 Archs: i386, x64 Package: biovizBase Version: 1.4.2 Depends: R (>= 2.10), methods Imports: methods, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, IRanges, GenomicRanges, Biostrings, Rsamtools, GenomicFeatures Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer License: Artistic-2.0 Archs: i386, x64 Package: birta Version: 1.0.0 Depends: limma, MASS, R(>= 2.10), Biobase, methods License: GPL (>= 2) Archs: i386, x64 Package: BitSeq Version: 1.0.1 Depends: Rsamtools, zlibbioc Imports: IRanges LinkingTo: Rsamtools, zlibbioc License: Artistic-2.0 Archs: i386, x64 Package: BRAIN Version: 1.0.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 Package: BrainStars Version: 1.0.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 Package: bridge Version: 1.20.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) Archs: i386, x64 Package: BSgenome Version: 1.24.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>= 1.13.6), GenomicRanges (>= 1.7.5), Biostrings (>= 2.23.3) Suggests: RUnit, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11), SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase License: Artistic-2.0 Package: BufferedMatrix Version: 1.20.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) Archs: i386, x64 Package: BufferedMatrixMethods Version: 1.20.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) Archs: i386, x64 Package: BUS Version: 1.12.0 Depends: R (>= 2.3.0), minet Imports: stats License: GPL-3 Archs: i386, x64 Package: CALIB Version: 1.22.0 Depends: R (>= 2.10), limma, methods Imports: limma, methods, graphics, stats, utils License: LGPL Archs: i386, x64 Package: CAMERA Version: 1.12.0 Depends: R (>= 2.1.0), methods, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit Enhances: Rmpi, snow License: GPL (>= 2) Archs: i386, x64 Package: CancerMutationAnalysis Version: 1.0.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE Archs: i386, x64 Package: Category Version: 2.22.0 Depends: AnnotationDbi (>= 0.1.15), Biobase (>= 1.15.29), methods Imports: graph, methods, Biobase (>= 1.15.29), AnnotationDbi (>= 0.1.15), RBGL, GSEABase, genefilter, annotate (>= 1.15.6), stats, utils Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, Matrix, KEGG.db, GO.db, SNPchip, geneplotter, limma, lattice, graph, Biobase, genefilter, methods License: Artistic-2.0 Package: categoryCompare Version: 1.0.2 Depends: R (>= 2.10), Biobase (>= 1.15.29), AnnotationDbi (>= 0.1.15), Category Imports: Biobase (>= 1.15.29), AnnotationDbi (>= 0.1.15), hwriter, GSEABase, Category (>= 2.21.2), 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: 1.0.0 Depends: R (>= 2.12.0), locfit (>= 1.5-4) Imports: lattice License: Artistic-2.0 Package: cellHTS Version: 1.26.0 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: 2.20.0 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: 1.2.0 Depends: RBGL, graph Suggests: Rgraphviz License: GPL-2 Package: CGEN Version: 1.8.0 Depends: R (>= 2.10.1), survival, cluster Suggests: cluster License: GPL-2 + file LICENSE Archs: i386, x64 Package: CGHbase Version: 1.14.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL Package: CGHcall Version: 2.16.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase License: GPL Package: cghMCR Version: 1.14.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL Package: CGHnormaliter Version: 1.10.0 Depends: CGHcall (>= 2.2.0), CGHbase (>= 1.2.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) Package: CGHregions Version: 1.14.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase License: GPL Package: charm Version: 2.2.0 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 License: LGPL (>= 2) Package: ChemmineR Version: 2.8.1 Depends: R (>= 2.10.0), methods Imports: graphics, methods, stats, RCurl License: Artistic-2.0 Package: ChIPpeakAnno Version: 2.4.0 Depends: R (>= 2.10), gplots, BiocGenerics (>= 0.1.0), biomaRt, multtest, IRanges, Biostrings, BSgenome, BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma Imports: gplots, BiocGenerics, biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db, limma, AnnotationDbi Suggests: reactome.db License: GPL (>= 2) Package: chipseq Version: 1.6.1 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: 1.10.0 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: 1.10.0 Depends: Biostrings Imports: IRanges, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) Package: chopsticks Version: 1.20.5 Depends: R(>= 2.10.0), survival, methods Suggests: hexbin License: GPL-3 Archs: i386, x64 Package: ChromHeatMap Version: 1.10.0 Depends: R (>= 2.9.0), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0), hgu95av2.db Imports: annotate, AnnotationDbi, Biobase, graphics, grDevices, methods, stats, IRanges, rtracklayer Suggests: ALL License: Artistic-2.0 Package: clippda Version: 1.6.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) Package: Clonality Version: 1.4.0 Depends: R (>= 2.12.2), DNAcopy Imports: DNAcopy, grDevices, graphics, stats, utils Suggests: gdata, DNAcopy License: GPL-3 Package: clst Version: 1.4.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 Package: clstutils Version: 1.4.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit, RSVGTipsDevice License: GPL-3 Package: clusterProfiler Version: 1.4.0 Depends: R (>= 2.10) Imports: methods, stats4, ggplot2, DBI, plyr, AnnotationDbi, GO.db, KEGG.db, org.Hs.eg.db, DOSE Suggests: GOSemSim, ReactomePA License: Artistic-2.0 Package: clusterStab Version: 1.28.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 Package: CMA Version: 1.14.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st License: GPL (>= 2) Package: CNAnorm Version: 1.2.0 Depends: R (>= 2.10.1), DNAcopy, methods Imports: methods License: GPL-2 Archs: i386, x64 Package: cn.farms Version: 1.4.0 Depends: R (>= 2.11), Biobase, methods, ff, oligoClasses, snowfall Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) Archs: i386, x64 Package: cn.mops Version: 1.2.6 Depends: R (>= 2.14), BiocGenerics (>= 0.1.0), Biobase, IRanges, GenomicRanges (>= 1.7.8) Imports: methods, graphics, BiocGenerics, IRanges, Rsamtools, Suggests: snow, DNAcopy License: LGPL (>= 2.0) Archs: i386, x64 Package: CNTools Version: 1.12.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL Archs: i386, x64 Package: cnvGSA Version: 1.0.0 Depends: methods Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL Package: CNVtools Version: 1.50.0 Depends: R (>= 2.10), survival License: GPL-3 Archs: i386, x64 Package: CoCiteStats Version: 1.28.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL Package: codelink Version: 1.24.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), limma Imports: annotate Suggests: genefilter Enhances: multicore License: GPL-2 Package: coGPS Version: 1.0.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 Package: ConsensusClusterPlus Version: 1.8.0 Imports: Biobase, ALL, graphics, stats, utils License: GPL-2 Package: convert Version: 1.32.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL Package: copa Version: 1.24.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 Archs: i386, x64 Package: Cormotif Version: 1.2.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 Package: coRNAi Version: 1.6.0 Depends: R (>= 2.10), cellHTS2, limma, locfit Imports: MASS, gplots, lattice, grDevices, graphics, stats License: Artistic-2.0 Package: CORREP Version: 1.22.0 Imports: e1071, stats Suggests: cluster, MASS License: GPL (>= 2) Package: cosmo Version: 1.22.0 Depends: R (>= 2.4.0), methods, utils, seqLogo Suggests: cosmoGUI License: file LICENSE Archs: i386, x64 Package: cosmoGUI Version: 1.22.0 Depends: tkWidgets, cosmo License: LGPL (>= 2) Package: cqn Version: 1.2.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 Package: CRImage Version: 1.6.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach License: Artistic-2.0 Package: crlmm Version: 1.14.3 Depends: R (>= 2.14.0), oligoClasses (>= 1.18.0) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), ellipse, genefilter (>= 1.37.1), mvtnorm, preprocessCore (>= 1.17.7), splines, stats, SNPchip, utils, lattice, ff, foreach Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.4), GGdata, snpStats, ellipse, RUnit License: Artistic-2.0 Archs: i386, x64 Package: CSAR Version: 1.8.0 Depends: R (>= 2.15.0), IRanges, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 Archs: i386, x64 Package: ctc Version: 1.30.0 Depends: amap License: GPL-2 Package: cummeRbund Version: 1.2.0 Depends: R (>= 2.7.0), RSQLite, ggplot2, reshape2 Imports: methods Suggests: cluster License: Artistic-2.0 Package: cycle Version: 1.10.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 Package: daMA Version: 1.28.0 Imports: MASS, stats License: GPL (>= 2) Package: DART Version: 1.2.1 Depends: R (>= 2.10.0), igraph0 Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 Package: DAVIDQuery Version: 1.16.0 Depends: RCurl (>= 1.4.0), utils License: GPL-2 Package: ddCt Version: 1.10.0 Depends: R (>= 2.3.0), Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, methods Suggests: RUnit License: LGPL-3 Package: DECIPHER Version: 1.2.0 Depends: R (>= 2.13.0), Biostrings (>= 2.16), RSQLite (>= 0.9), IRanges, stats Imports: Biostrings, RSQLite, IRanges, stats LinkingTo: Biostrings, RSQLite, IRanges, stats License: GPL-3 Archs: i386, x64 Package: DEDS Version: 1.30.0 Depends: R (>= 1.7.0) License: LGPL Archs: i386, x64 Package: deepSNV Version: 1.2.3 Depends: R (>= 2.13.0), Rsamtools (>= 1.4.3), GenomicRanges, IRanges, Biostrings, VGAM, methods, graphics Imports: Rsamtools LinkingTo: Rsamtools License: GPL-3 Archs: i386, x64 Package: DEGraph Version: 1.8.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 Package: DEGseq Version: 1.10.0 Depends: R (>= 2.8.0), qvalue, samr, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) Archs: i386, x64 Package: DESeq Version: 1.8.3 Depends: Biobase (>= 2.13.11), locfit Imports: genefilter, geneplotter, methods, MASS Suggests: pasilla (>= 0.2.11), vsn License: GPL (>= 3) Archs: i386, x64 Package: DEXSeq Version: 1.2.1 Depends: Biobase (>= 2.13.11) Imports: biomaRt, hwriter, methods, stringr, statmod (>= 1.4.15) Suggests: pasilla (>= 0.2.6) Enhances: multicore License: GPL (>= 3) Package: DFP Version: 1.14.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 Package: DiffBind Version: 1.2.4 Depends: R (>= 2.14.0), GenomicRanges Imports: RColorBrewer, amap, edgeR (>= 2.3.58), gplots, limma, DESeq, grDevices, stats, utils, IRanges, zlibbioc LinkingTo: Rsamtools Suggests: DESeq Enhances: rgl, parallel License: Artistic-2.0 Archs: i386, x64 Package: diffGeneAnalysis Version: 1.38.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL Package: dks Version: 1.2.0 Depends: R (>= 2.8) Imports: cubature License: GPL Package: DNAcopy Version: 1.30.0 License: GPL (>= 2) Archs: i386, x64 Package: domainsignatures Version: 1.16.0 Depends: R (>= 2.4.0), KEGG.db, prada, biomaRt, methods Imports: AnnotationDbi License: Artistic-2.0 Package: DOSE Version: 1.2.1 Depends: R (>= 2.10) Imports: methods, plyr, qvalue, stats4, AnnotationDbi, DO.db, org.Hs.eg.db, igraph, scales, ggplot2, graphics Suggests: clusterProfiler, GOSemSim, ReactomePA License: Artistic-2.0 Package: DTA Version: 2.2.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 Package: dualKS Version: 1.16.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.0), affy, methods License: LGPL (>= 2.0) Package: dyebias Version: 1.14.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 Package: DynDoc Version: 1.34.0 Depends: methods, utils Imports: methods License: Artistic-2.0 Package: easyRNASeq Version: 1.2.5 Depends: graphics, methods, parallel, utils, genomeIntervals (>= 1.12.0), Biobase (>= 2.16.0), BiocGenerics (>= 0.2.0), biomaRt (>= 2.12.0), edgeR (>= 2.6.10), Biostrings (>= 2.24.1), BSgenome (>= 1.24.0), DESeq (>= 1.8.3), GenomicRanges (>= 1.8.12), IRanges (>= 1.14.4), Rsamtools (>= 1.8.6), ShortRead (>= 1.14.4) Suggests: BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), GenomicFeatures (>= 1.8.2), RnaSeqTutorial (>= 0.0.8) Enhances: edgeR, genomeIntervals, DESeq, ShortRead License: Artistic-2.0 Package: EBarrays Version: 2.20.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) Archs: i386, x64 Package: EBcoexpress Version: 1.0.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) Archs: i386, x64 Package: EBImage Version: 3.12.0 Depends: R (>= 2.8.0), methods, graphics, stats, utils, abind License: Artistic-2.0 Archs: i386, x64 Package: ecolitk Version: 1.28.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest License: GPL (>= 2) Package: EDASeq Version: 1.2.0 Depends: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), ShortRead (>= 1.11.42), Rsamtools (>= 1.5.75), aroma.light Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq Suggests: yeastRNASeq, leeBamViews, edgeR, DESeq License: Artistic-2.0 Package: edgeR Version: 2.6.12 Depends: R (>= 2.3.0), methods, limma Suggests: MASS, statmod, splines License: LGPL (>= 2) Package: eisa Version: 1.8.2 Depends: methods, isa2, Biobase, AnnotationDbi, Category, genefilter, DBI Suggests: igraph0 (>= 0.5.5), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db License: GPL (>= 2) Package: ENVISIONQuery Version: 1.4.0 Depends: rJava, XML, utils License: GPL-2 Package: ExiMiR Version: 1.4.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1) Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) License: GPL-2 Package: exomeCopy Version: 1.2.0 Depends: IRanges, GenomicRanges, Rsamtools Imports: stats4, methods Suggests: Biostrings License: GPL (>= 2) Archs: i386, x64 Package: explorase Version: 1.20.0 Depends: R (>= 2.6.2) Imports: limma, rggobi, RGtk2 Suggests: cairoDevice License: GPL-2 Package: ExpressionView Version: 1.8.0 Depends: caTools, bitops Imports: methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Suggests: ALL, hgu95av2.db, biclust, GO.db, KEGG.db, AnnotationDbi, affy License: GPL (>= 2) Archs: i386, x64 Package: externalVector Version: 1.22.0 Depends: R (>= 1.8.0), methods, stats License: LGPL Archs: i386, x64 Package: fabia Version: 2.2.2 Depends: R (>= 2.8.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) Archs: i386, x64 Package: factDesign Version: 1.32.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter License: LGPL Package: farms Version: 1.8.2 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: 1.2.3 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: graphics, stats, IRanges, BiocGenerics Suggests: DNAcopy, oligo, License: LGPL (>= 2.0) Archs: i386, x64 Package: fdrame Version: 1.28.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: ffpe Version: 1.0.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, affy, ffpeExampleData License: GPL (> 2) Package: flagme Version: 1.12.0 Depends: gcspikelite, xcms Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) Archs: i386, x64 Package: flowClust Version: 2.14.0 Depends: R(>= 2.5.0),BiocGenerics, methods, mnormt, ellipse, Biobase, flowCore(>= 1.11.23) Imports: stats4 Suggests: snowfall Enhances: multicore License: Artistic-2.0 Archs: i386, x64 Package: flowCore Version: 1.22.3 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: 1.14.0 Depends: R (>= 2.5.0), MASS, Imports: flowCore, XML (>= 1.96), methods, Biobase License: GPL (>= 3) Package: flowFP Version: 1.14.0 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: 1.8.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 Package: flowMerge Version: 2.4.0 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: flowPhyto Version: 1.8.0 Depends: R (>= 1.8.0) Imports: caroline, flowClust, flowCore, flowMeans, TTR Suggests: RPostgreSQL, zoo, maps, mapdata, plotrix License: Artistic-2.0 Package: flowPlots Version: 1.4.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 Package: flowQ Version: 1.16.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.1.3), outliers, lattice, flowViz, mvoutlier, bioDist, parody, RColorBrewer, latticeExtra Imports: methods, BiocGenerics, geneplotter, flowCore, flowViz, IRanges Suggests: flowStats License: Artistic-2.0 Package: flowStats Version: 1.14.0 Depends: R (>= 2.10), flowCore (>= 1.10.0), fda (>= 2.2.6), mvoutlier, cluster, flowWorkspace Imports: BiocGenerics, MASS, flowViz, flowCore, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, utils, KernSmooth, lattice,compositions Suggests: flowViz, xtable Enhances: RBGL,ncdfFlow,graph License: Artistic-2.0 Package: flowTrans Version: 1.8.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 Package: flowType Version: 1.2.0 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: 1.16.0 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: 1.20.0 Depends: R (>= 2.7.0), flowCore (>= 1.5.17), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils Suggests: RColorBrewer, IDPmisc,colorspace License: Artistic-2.0 Archs: i386, x64 Package: flowWorkspace Version: 1.2.0 Depends: Cairo, BiocGenerics, methods, RBGL, graph, XML, flowCore, flowViz, Biobase, IDPmisc, tools,hexbin Imports: Biobase, XML, flowCore, graph, graphics, lattice, methods, stats, stats4, utils Suggests: testthat, flowWorkspaceData, Rgraphviz Enhances: multicore,Rmpi,ncdfFlow License: Artistic-2.0 Archs: i386, x64 Package: frma Version: 1.8.0 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: 1.8.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) Package: gaga Version: 2.2.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: multicore License: GPL (>= 2) Archs: i386, x64 Package: gage Version: 2.6.0 Depends: R (>= 2.10), graph, multtest Suggests: gageData, GO.db, GSEABase, KEGG.db, org.Hs.eg.db License: GPL (>= 2.0) Package: gaggle Version: 1.24.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) Package: gaia Version: 1.10.2 Depends: R (>= 2.10) License: GPL-2 Package: gcrma Version: 2.28.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils, BiocInstaller Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), IRanges, Biostrings (>= 2.11.32), splines Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL Archs: i386, x64 Package: genArise Version: 1.32.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE Package: gene2pathway Version: 2.10.1 Depends: R (>= 2.10.0), kernlab (>= 0.9), biomaRt (>= 1.12.1), KEGGSOAP (>= 1.12.0), RBGL, AnnotationDbi,org.Dm.eg.db, keggorthology (>= 2.0) Imports: SSOAP, RCurl Enhances: doMC License: GPL (>= 2) Package: GeneAnswers Version: 1.12.2 Depends: R (>= 2.10.0), igraph0, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, rgl, Heatplus, RColorBrewer Imports: graph, Rgraphviz, RBGL, annotate Suggests: GO.db, KEGG.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db License: LGPL (>= 2) Package: GeneExpressionSignature Version: 1.2.0 Depends: Biobase License: GPL-2 Package: genefilter Version: 1.38.0 Imports: AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10), graphics, methods, stats, survival Suggests: Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets, ALL, ROC License: Artistic-2.0 Archs: i386, x64 Package: genefu Version: 1.6.1 Depends: R (>= 2.10), survcomp, mclust Imports: amap Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable License: Artistic-2.0 Package: GeneGroupAnalysis Version: 1.2.0 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: 1.28.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) License: Artistic-2.0 Package: geneplotter Version: 1.34.0 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: 1.28.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) Package: GeneRegionScan Version: 1.12.0 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: 1.12.0 Depends: R (>= 2.13.2), Biobase Imports: Biobase, MASS, graphics, stats, survival, limma Suggests: ALL License: GPL (>= 2) Package: GeneSelector Version: 2.6.0 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: GeneticsDesign Version: 1.24.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 Package: GeneticsPed Version: 1.18.0 Depends: R (>= 2.4.0), gdata (>= 2.3.0), genetics (>= 1.3.0), MASS Suggests: RUnit, gtools License: LGPL (>= 2.1) Archs: i386, x64 Package: genoCN Version: 1.8.0 Imports: graphics, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: GenomeGraphs Version: 1.16.0 Depends: R (>= 2.10), methods, biomaRt, grid License: Artistic-2.0 Package: genomeIntervals Version: 1.12.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.13.3), BiocGenerics (>= 0.1.11) Imports: methods, Biobase License: Artistic-2.0 Package: genomes Version: 2.2.0 Depends: R (>= 2.10), XML License: Artistic-2.0 Package: GenomicFeatures Version: 1.8.3 Depends: BiocGenerics (>= 0.1.0), IRanges (>= 1.13.10), GenomicRanges (>= 1.7.17), AnnotationDbi (>= 1.15.39) Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics, IRanges, GenomicRanges, Biostrings (>= 2.23.2), rtracklayer (>= 1.15.1), biomaRt, RCurl, utils, Biobase (>= 2.15.1) Suggests: rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14), BSgenome.Celegans.UCSC.ce2, mirbase.db, FDb.UCSC.tRNAs, RUnit, TxDb.Hsapiens.UCSC.hg18.knownGene License: Artistic-2.0 Package: GenomicRanges Version: 1.8.13 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.12), IRanges (>= 1.13.36) Imports: methods, BiocGenerics, IRanges LinkingTo: IRanges Suggests: Rsamtools (>= 1.7.42), BSgenome, rtracklayer, GenomicFeatures, EatonEtAlChIPseq (>= 0.0.3), leeBamViews, edgeR, DESeq, rtracklayer, org.Sc.sgd.db, BSgenome.Scerevisiae.UCSC.sacCer2, DEXSeq, pasilla, pasillaBamSubset, VariantAnnotation, RUnit License: Artistic-2.0 Archs: i386, x64 Package: Genominator Version: 1.10.0 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: 1.6.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.6), Biobase (>= 2.15.1), IRanges (>= 1.13.5), bigmemory, GenomicRanges Imports: methods, BiocGenerics, Biobase, DNAcopy, graphics, IRanges, stats, GenomicRanges, Biostrings, BSgenome, bigmemory Suggests: RUnit Enhances: parallel, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 Archs: i386, x64 Package: GEOmetadb Version: 1.16.0 Depends: GEOquery,RSQLite License: Artistic-2.0 Package: GEOquery Version: 2.23.5 Depends: methods, Biobase Imports: XML, RCurl Suggests: limma, RUnit License: GPL-2 Package: GEOsubmission Version: 1.8.0 Imports: affy, Biobase, utils License: GPL (>= 2) Package: GEWIST Version: 1.0.0 Depends: R (>= 2.10), car License: GPL-2 Package: GGBase Version: 3.18.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, Matrix, AnnotationDbi License: Artistic-2.0 Package: ggbio Version: 1.4.6 Depends: methods, ggplot2 (>= 0.9) Imports: methods, biovizBase(>= 1.4.2), reshape2, ggplot2(>= 0.9), BiocGenerics, Biobase, IRanges, GenomicRanges, GenomicFeatures, Rsamtools, BSgenome, gridExtra, scales, plyr, VariantAnnotation, Hmisc, rtracklayer Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, affyPLM License: Artistic-2.0 Package: GGtools Version: 4.4.0 Depends: R (>= 2.14), stats4, GGBase (>= 3.16.1), IRanges, GenomicRanges, Rsamtools Imports: methods, utils, stats, BiocGenerics, snpStats, ff, AnnotationDbi, Biobase, bit, VariantAnnotation Suggests: GGdata, illuminaHumanv1.db Enhances: MatrixEQTL License: Artistic-2.0 Package: girafe Version: 1.8.0 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: 2.18.0 Depends: R (>= 2.10) Suggests: aws, tcltk License: GPL-2 Archs: i386, x64 Package: GlobalAncova Version: 3.24.0 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: 5.10.0 Depends: methods Imports: Biobase (>= 2.5.5), survival, AnnotationDbi, annotate, multtest, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, annotate, Biobase (>= 2.5.5), survival, GSEABase, penalized, gss, MASS, boot, rpart License: GPL (>= 2) Package: GOFunction Version: 1.2.0 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: 1.18.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db License: GPL-2 Package: GOSemSim Version: 1.14.0 Depends: R (>= 2.10) Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db Suggests: DOSE, clusterProfiler License: GPL-2 Package: goseq Version: 1.8.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase Imports: mgcv, graphics, stats, utils, AnnotationDbi Suggests: GO.db, edgeR, org.Hs.eg.db License: LGPL (>= 2) Package: GOstats Version: 2.22.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.3.26), graph Imports: AnnotationDbi (>= 0.0.89), Biobase (>= 1.15.29), Category (>= 2.3.26), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), graph (>= 1.15.15), methods, stats Suggests: hgu95av2.db (>= 1.13.0), ALL, GO.db (>= 1.13.0), annotate, multtest, genefilter, RColorBrewer, Rgraphviz, xtable, SparseM License: Artistic-2.0 Package: goTools Version: 1.30.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 Package: gpls Version: 1.28.0 Imports: stats Suggests: MASS License: Artistic-2.0 Package: gprege Version: 1.0.0 Depends: R (>= 2.8.0), gptk Suggests: spam License: AGPL-3 Package: graph Version: 1.34.0 Depends: R (>= 2.10), methods Imports: methods, stats, tools, utils, BiocGenerics (>= 0.1.11) Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster Enhances: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Package: GraphAlignment Version: 1.18.0 License: file LICENSE Archs: i386, x64 Package: GraphAT Version: 1.28.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL Package: graphite Version: 1.2.0 Depends: R (>= 2.10), graph Imports: AnnotationDbi, graph, graphics, methods, org.Hs.eg.db, stats, utils Suggests: DEGraph (>= 1.4), hgu133plus2.db, RCytoscape (>= 1.2), SPIA (>= 2.2), topologyGSA (>= 1.0) License: AGPL-3 Package: GRENITS Version: 1.10.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) Archs: i386, x64 Package: GSEABase Version: 1.18.0 Depends: R (>= 2.6.0), BiocGenerics, Biobase, annotate, methods, graph Imports: BiocGenerics, annotate, AnnotationDbi, Biobase, graph, methods, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz License: Artistic-2.0 Package: GSEAlm Version: 1.16.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 Package: GSRI Version: 2.4.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: multicore License: GPL-3 Package: GSVA Version: 1.4.4 Depends: R (>= 2.13.0), methods, GSEABase (>= 1.18.0) Imports: methods, Biobase, GSEABase Suggests: limma, qpgraph, RBGL, graph, Rgraphviz, RColorBrewer, genefilter, mclust, edgeR, GSVAdata Enhances: snow, parallel License: GPL (>= 2) Archs: i386, x64 Package: Gviz Version: 1.0.1 Depends: R (>= 2.10.0), methods, grid Imports: IRanges (>= 1.13.19), rtracklayer (>= 1.15.5), lattice, RColorBrewer, biomaRt (>= 2.11.0), GenomicRanges (>= 1.7.14), AnnotationDbi (>= 1.17.11), Biobase (>= 2.15.3), BiocGenerics (>= 0.1.4) Suggests: xtable License: Artistic-2.0 Package: gwascat Version: 1.0.0 Depends: R (>= 2.14.0), methods, IRanges, GenomicRanges, snpStats, graph Imports: Biostrings Suggests: DO.db Enhances: SNPlocs.Hsapiens.dbSNP.20110815, pd.genomewidesnp.6 License: Artistic-2.0 Package: GWASTools Version: 1.2.1 Depends: Biobase, ncdf, GWASExactHW, sandwich Imports: methods, DBI, RSQLite, DNAcopy, survival, lmtest Suggests: GWASdata, RUnit, gdsfmt, SNPRelate License: Artistic-2.0 Package: Harshlight Version: 1.28.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: Heatplus Version: 2.2.0 Imports: graphics, grDevices, stats Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) Package: HELP Version: 1.14.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) Package: HEM Version: 1.28.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: HilbertVis Version: 1.14.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) Archs: i386, x64 Package: HilbertVisGUI Version: 1.14.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) Archs: i386, x64 Package: HiTC Version: 1.0.0 Depends: R (>= 2.10.0), methods, girafe (>= 1.3.1), genomeIntervals (>= 1.7.1), RColorBrewer Imports: methods, Biobase, Biostrings, graphics, grDevices, ShortRead License: Artistic-2.0 Package: hopach Version: 2.16.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: Biobase, cluster, graphics, grDevices, methods, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: HTqPCR Version: 1.10.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 Package: HTSanalyzeR Version: 2.8.3 Depends: R (>= 2.10), igraph0, GSEABase, BioNet, cellHTS2, RankProd, methods Imports: graph, igraph0, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow License: Artistic-2.0 Package: htSeqTools Version: 1.2.0 Depends: R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase, IRanges, methods, MASS, BSgenome, GenomicRanges Enhances: multicore License: GPL (>= 2) Package: HybridMTest Version: 1.0.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) Package: hyperdraw Version: 1.8.0 Depends: R (>= 2.9.0), methods, grid, graph, hypergraph, Rgraphviz Imports: stats4 License: GPL (>= 2) Package: hypergraph Version: 1.28.0 Depends: R (>= 2.1.0), methods, graph License: Artistic-2.0 Package: iASeq Version: 1.0.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 Package: iBBiG Version: 1.0.2 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 Archs: i386, x64 Package: ibh Version: 1.4.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) Package: Icens Version: 1.28.0 Depends: survival Imports: graphics License: Artistic-2.0 Package: iChip Version: 1.10.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) Archs: i386, x64 Package: idiogram Version: 1.32.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 Package: IdMappingAnalysis Version: 1.0.1 Depends: R (>= 2.14), R.oo, rChoiceDialogs Imports: boot, mclust, RColorBrewer, Biobase License: GPL-2 Package: IdMappingRetrieval Version: 1.2.0 Depends: R.oo, XML, RCurl, rChoiceDialogs, ENVISIONQuery Imports: biomaRt, ENVISIONQuery, DAVIDQuery, AffyCompatible, R.methodsS3, R.oo, utils License: GPL-2 Package: imageHTS Version: 1.6.0 Depends: R (>= 2.9.0), EBImage (>= 3.7.1), cellHTS2 (>= 2.10.0) Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071 License: LGPL-2.1 Package: impute Version: 1.30.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: inSilicoDb Version: 1.4.0 Depends: R (>= 2.11.0), rjson, Biobase Imports: RCurl License: GPL-2 Package: inSilicoMerging Version: 1.0.8 Depends: R (>= 2.11.1), Biobase, DWD, limma Imports: amap, moments Suggests: BiocGenerics, inSilicoDb License: GPL-2 Package: inveRsion Version: 1.4.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) Archs: i386, x64 Package: iontree Version: 1.2.0 Depends: methods, rJava, RSQLite, XML Suggests: iontreeData License: GPL-2 Package: IPPD Version: 1.4.0 Depends: R (>= 2.12.0), MASS, Matrix, XML, digest, bitops Imports: methods, stats, graphics License: GPL (>= 2) Archs: i386, x64 Package: IRanges Version: 1.14.4 Depends: R (>= 2.8.0), methods, utils, stats, BiocGenerics (>= 0.1.4) Imports: methods, utils, stats, BiocGenerics, stats4 Suggests: RUnit License: Artistic-2.0 Archs: i386, x64 Package: iSeq Version: 1.8.0 Depends: R (>= 2.10.0) License: GPL (>= 2) Archs: i386, x64 Package: isobar Version: 1.2.1 Depends: R (>= 2.10.0), Biobase, stats, methods, plyr Imports: distr Suggests: MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2 License: LGPL-2 Package: IsoGeneGUI Version: 1.12.0 Depends: tcltk, tkrplot, IsoGene Imports: multtest, relimp, WriteXLS,gdata, RColorBrewer, geneplotter Suggests: RUnit License: GPL-2 Package: ITALICS Version: 2.16.0 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 Package: iterativeBMA Version: 1.14.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) Package: iterativeBMAsurv Version: 1.14.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) Package: joda Version: 1.4.0 Depends: R (>= 2.0), bgmm, RBGL License: GPL (>= 2) Package: KCsmart Version: 2.14.0 Depends: methods, siggenes, multtest, KernSmooth Enhances: Biobase, CGHbase License: GPL-3 Package: KEGGgraph Version: 1.12.0 Depends: R (>= 2.10), methods, XML (>= 2.3-0), graph Imports: methods, XML, graph Suggests: Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) Package: keggorthology Version: 2.8.0 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 Package: KEGGSOAP Version: 1.30.4 Depends: methods, BiocGenerics Imports: XML, RCurl, SSOAP (>= 0.2-2), XMLSchema Suggests: RUnit License: BSD Package: lapmix Version: 1.22.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) Package: LBE Version: 1.24.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue License: GPL-2 Package: les Version: 1.6.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: multicore License: GPL-3 Package: limma Version: 3.12.3 Depends: R (>= 2.3.0), methods Suggests: affy, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn License: GPL (>= 2) Archs: i386, x64 Package: limmaGUI Version: 1.32.0 Depends: limma, tcltk Suggests: statmod, R2HTML, xtable, tkrplot License: LGPL Package: LiquidAssociation Version: 1.10.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) Package: LMGene Version: 2.12.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy Suggests: affydata License: LGPL Package: logicFS Version: 1.26.0 Depends: LogicReg, mcbiopi Suggests: genefilter, siggenes License: LGPL (>= 2) Package: logitT Version: 1.14.0 Depends: affy Suggests: SpikeInSubset License: GPL (>= 2) Archs: i386, x64 Package: lol Version: 1.4.0 Depends: penalized, Matrix Imports: Matrix, penalized, graphics, grDevices, stats License: GPL-2 Package: LPE Version: 1.30.0 Depends: R (>= 2.10) Imports: stats License: LGPL Package: LPEadj Version: 1.16.0 Depends: LPE Imports: LPE, stats License: LGPL Package: lumi Version: 2.8.0 Depends: R (>= 2.10), methylumi (>= 1.7.4), Biobase (>= 2.5.5), nleqslv Imports: affy (>= 1.23.4), methylumi, genoset, GenomicRanges, IRanges, rtracklayer, annotate, Biobase (>= 2.5.5), mgcv (>= 1.4-0), hdrcde, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) Package: LVSmiRNA Version: 1.6.0 Depends: R (>= 2.10), Biobase,quantreg,splines,MASS,limma,affy,methods, SparseM, vsn Imports: BiocGenerics, stats4 Enhances: multicore,snow, Rmpi License: GPL-2 Archs: i386, x64 Package: maanova Version: 1.26.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, stats, utils Suggests: qvalue, snow Enhances: Rmpi License: GPL (>= 2) Archs: i386, x64 Package: macat Version: 1.30.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem License: Artistic-2.0 Package: maCorrPlot Version: 1.26.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) Package: made4 Version: 1.30.0 Depends: ade4, RColorBrewer,gplots,scatterplot3d Suggests: affy License: Artistic-2.0 Package: maigesPack Version: 1.20.0 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) Archs: i386, x64 Package: makecdfenv Version: 1.34.0 Depends: R (>= 2.6.0), methods Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) Archs: i386, x64 Package: MANOR Version: 1.28.0 Depends: R (>= 2.10), GLAD Imports: GLAD, graphics, grDevices, stats, utils License: GPL-2 Archs: i386, x64 Package: manta Version: 1.2.0 Depends: R (>= 1.8.0), methods, edgeR (>= 2.5.13) Imports: Hmisc, caroline(>= 0.6.6) Suggests: RSQLite, plotrix License: Artistic-2.0 Package: MantelCorr Version: 1.26.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) Package: marray Version: 1.34.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL Package: maSigPro Version: 1.28.0 Depends: R (>= 2.3.1), stats, Biobase Imports: Biobase, graphics, grDevices, limma, Mfuzz, stats, utils License: GPL (>= 2) Package: maskBAD Version: 1.0.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe License: GPL (>= 2) Package: MassArray Version: 1.8.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, methods, stats, utils License: GPL (>= 2) Package: MassSpecWavelet Version: 1.22.0 Depends: waveslim Suggests: xcms, caTools License: LGPL (>= 2) Archs: i386, x64 Package: MBCB Version: 1.10.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) Package: mBPCR Version: 1.10.0 Depends: oligoClasses, SNPchip Imports: Biobase Suggests: xtable License: GPL (>= 2) Package: mcaGUI Version: 1.4.0 Depends: lattice, MASS, proto, foreign, gWidgets(>= 0.0-36), gWidgetsRGtk2(>= 0.0-53), OTUbase, vegan, bpca Enhances: iplots, reshape, ggplot2, cairoDevice, OTUbase License: GPL (>= 2) Package: MCRestimate Version: 2.12.0 Depends: R (>= 2.7.2), golubEsets (>= 1.4.6) Imports: e1071 (>= 1.5-12), pamr (>= 1.22), randomForest (>= 3.9-6), RColorBrewer (>= 0.1-3), Biobase (>= 2.5.5), graphics, grDevices, stats, utils Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0), gpls (>= 1.6.0) License: GPL (>= 2) Package: mdqc Version: 1.18.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) Package: MeasurementError.cor Version: 1.28.0 License: LGPL Package: MEDIPS Version: 1.6.0 Depends: R (>= 2.12.0), BiocGenerics (>= 0.1.3), BSgenome Imports: methods, BiocGenerics, Biostrings, BSgenome, graphics, gtools, IRanges, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19 License: GPL (>= 2) Archs: i386, x64 Package: MEDME Version: 1.16.3 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) Archs: i386, x64 Package: MergeMaid Version: 2.28.0 Depends: R (>= 2.2.0), survival, Biobase, MASS, methods License: GPL (>= 2) Package: metaArray Version: 1.34.0 Imports: Biobase, MergeMaid, graphics, stats License: LGPL-2 Archs: i386, x64 Package: metahdep Version: 1.14.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 Archs: i386, x64 Package: methVisual Version: 1.8.0 Depends: R (>= 2.11.0), Biostrings(>= 2.4.8), plotrix,gsubfn, grid,sqldf Imports: Biostrings, ca, graphics, grDevices, grid, gridBase, IRanges, stats, utils License: GPL (>= 2) Package: methylumi Version: 2.2.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2 Imports: Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, stats4, BiocGenerics Suggests: lumi, lattice, limma, xtable, IlluminaHumanMethylation27k.db (>= 1.4.4), IlluminaHumanMethylation450k.db, SQN, MASS, matrixStats, parallel License: GPL-2 Package: Mfuzz Version: 2.14.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 Package: mgsa Version: 1.4.0 Depends: R (>= 2.9.0), methods, gplots Imports: gplots, graphics, stats, utils Suggests: DBI, RSQLite, GO.db License: Artistic-2.0 Archs: i386, x64 Package: MiChip Version: 1.10.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) Package: microRNA Version: 1.14.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) Suggests: Biostrings (>= 2.11.32) Enhances: Rlibstree License: Artistic-2.0 Package: minet Version: 3.10.0 Depends: infotheo License: file LICENSE Archs: i386, x64 Package: minfi Version: 1.2.0 Depends: methods, BiocGenerics (>= 0.1.0), Biobase (>= 2.15.1), lattice, reshape, GenomicRanges Imports: beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, crlmm, matrixStats, mclust Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), minfiData (>= 0.2.0), Biostrings License: Artistic-2.0 Package: MinimumDistance Version: 1.0.0 Depends: R (>= 2.14), IRanges (>= 1.13.30) Imports: methods, DNAcopy, utils, msm, lattice, BiocGenerics, VanillaICE (>= 1.17.22), ff, SNPchip (>= 2.0.3), Biobase, foreach, oligoClasses (>= 1.17.38) Suggests: human610quadv1bCrlmm, RUnit Enhances: snow, doSNOW License: Artistic-2.0 Package: MiPP Version: 1.28.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) Package: miRNApath Version: 1.16.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 Package: MLInterfaces Version: 1.36.1 Depends: R (>= 2.9), Biobase, MASS, methods, genefilter, rpart, rda, annotate, cluster, sfsmisc Imports: mboost, gdata 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: 1.4.2 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: MmPalateMiRNA Version: 1.4.0 Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod, lattice, vsn Imports: limma, lattice, Biobase Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra License: LGPL-3 Package: mosaics Version: 1.4.1 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: motifRG Version: 1.0.0 Depends: R (>= 2.10) Imports: Biostrings, IRanges, seqLogo, parallel, methods, grid,graphics License: Artistic-2.0 Package: MotIV Version: 1.10.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.0) Imports: graphics, grid, methods, BiocGenerics, IRanges (>= 1.13.5), lattice, rGADEM, stats, utils Suggests: rtracklayer License: GPL-2 Archs: i386, x64 Package: MSnbase Version: 1.4.1 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.3), Biobase (>= 2.15.2), ggplot2, mzR Imports: graphics, plyr, IRanges, preprocessCore, vsn, grid, reshape Suggests: testthat, zoo, pgfSweave, Rdisop Enhances: foreach, doMC License: Artistic-2.0 Package: Mulcom Version: 1.6.0 Depends: R (>= 2.10), fields, Biobase Imports: graphics, grDevices, stats, methods License: GPL-2 Archs: i386, x64 Package: multiscan Version: 1.16.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) Archs: i386, x64 Package: multtest Version: 2.12.0 Depends: R (>= 2.10), methods, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL Archs: i386, x64 Package: MVCClass Version: 1.30.0 Depends: R (>= 2.1.0), methods License: LGPL Package: mzR Version: 1.2.2 Depends: Rcpp (>= 0.9.4), methods Imports: Biobase LinkingTo: Rcpp Suggests: msdata, RUnit, faahKO License: Artistic-2.0 Archs: i386, x64 Package: NarrowPeaks Version: 1.0.1 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: 1.4.0 Depends: graph, R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCytoscape, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 Package: nem Version: 2.32.1 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), Rgraphviz (>= 1.22), plotrix, limma, cluster (>= 1.11), statmod, Hmisc Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, Rgraphviz, stats, utils Suggests: Biobase (>= 1.10) Enhances: doMC License: GPL (>= 2) Archs: i386, x64 Package: netresponse Version: 1.8.0 Depends: R (>= 2.14.1), methods, igraph, graph, minet, qvalue, parallel, RColorBrewer, Rgraphviz, ggplot2 License: GPL (>= 2) Archs: i386, x64 Package: nnNorm Version: 2.20.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL Package: NormqPCR Version: 1.2.0 Depends: R(>= 2.10.0), stats, RColorBrewer, Biobase, methods, ReadqPCR Imports: ReadqPCR License: LGPL-3 Package: NTW Version: 1.6.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 Package: nucleR Version: 1.4.0 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: 1.22.0 Imports: stats License: GPL-2 Package: NuPoP Version: 1.6.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: occugene Version: 1.16.0 Depends: R (>= 2.0.0) License: GPL (>= 2) Package: OCplus Version: 1.30.0 Depends: R (>= 2.1.0), akima Imports: multtest (>= 1.7.3), graphics, grDevices, stats License: LGPL Package: oligo Version: 1.20.4 Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35) Imports: affyio (>= 1.23.2), affxparser (>= 1.27.5), Biobase (>= 2.15.4), Biostrings (>= 2.23.6), BiocGenerics (>= 0.1.14), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore (>= 1.17.7), 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: 1.18.0 Depends: R (>= 2.14) Imports: Biobase (>= 2.15.1), methods, graphics, BiocGenerics (>= 0.1.14), IRanges (>= 1.13.30), Biostrings (>= 2.23.6), affyio (>= 1.23.2), ff, foreach, BiocInstaller, utils Suggests: RSQLite, hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm, genomewidesnp5Crlmm, VanillaICE, RUnit Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) Package: OLIN Version: 1.34.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 Package: OLINgui Version: 1.30.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 Package: oneChannelGUI Version: 1.22.12 Depends: Biobase, affylmGUI, tkWidgets, IRanges, Rsamtools, Biostrings, siggenes Suggests: annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno, chipseq, BSgenome, Rgraphviz, affy ,annaffy, affyPLM, multtest, ssize, sizepower, RankProd, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, edgeR, metaArray, MergeMaid, biomaRt, GenomeGraphs,AffyCompatible, rtracklayer, Genominator, EDASeq, limma, DESeq, goseq, cummeRbund, 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 License: Artistic-2.0 Package: ontoCAT Version: 1.8.0 Depends: rJava, methods License: Apache License 2.0 Package: OrderedList Version: 1.28.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2), methods Imports: Biobase, graphics, methods, stats, twilight License: GPL (>= 2) Package: OTUbase Version: 1.6.0 Depends: R (>= 2.9.0), methods, ShortRead (>= 1.4.0), Biobase, vegan Imports: Biostrings, ShortRead, IRanges License: Artistic-2.0 Package: OutlierD Version: 1.20.0 Depends: R (>= 2.3.0), Biobase, quantreg License: GPL (>= 2) Package: PAnnBuilder Version: 1.20.0 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: 1.26.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils License: GPL (>= 2) Package: PANR Version: 1.2.3 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils Suggests: snow, RedeR License: Artistic-2.0 Package: parody Version: 1.14.0 Depends: R (>= 2.5.0), methods, tools, utils License: Artistic-2.0 Package: pathRender Version: 1.24.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods Suggests: ALL, hgu95av2.db License: LGPL Package: PatientGeneSets Version: 1.6.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2.0) Archs: i386, x64 Package: pcaGoPromoter Version: 1.0.0 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: 1.42.0 Depends: Biobase, MASS, pls, methods, Rcpp (>= 0.8.7) Imports: BiocGenerics LinkingTo: Rcpp Suggests: aroma.light License: GPL (>= 3) Archs: i386, x64 Package: pcot2 Version: 1.24.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800.db, KEGG.db, mvtnorm License: GPL (>= 2) Package: PCpheno Version: 1.18.0 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: 1.20.0 Depends: R (>= 2.11.0), methods, Biobase (>= 2.5.5), RSQLite (>= 0.7-1), affxparser (>= 1.7.3), oligo (>= 1.9.19) Imports: Biostrings (>= 2.13.50), IRanges (>= 1.3.89) License: Artistic-2.0 Archs: i386, x64 Package: pdmclass Version: 1.28.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda License: Artistic-2.0 Package: PGSEA Version: 1.30.0 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: 1.4.0 Depends: R (>= 2.9.0), imageHTS, e1071 Suggests: GOstats, MASS License: LGPL-2.1 Package: phenoTest Version: 1.4.0 Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR Suggests: GSEABase, KEGG.db, GO.db Enhances: multicore, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) Package: phyloseq Version: 1.0.3 Depends: R (>= 2.15.0), methods, ade4 (>= 1.4), ape (>= 2.8), ggplot2 (>= 0.9.2), picante (>= 1.3), reshape (>= 0.8.4) Imports: foreach (>= 1.3), igraph0 (>= 0.5), multtest (>= 2.8), plyr (>= 1.7), RJSONIO (>= 0.98), vegan (>= 2.0) Suggests: genefilter Enhances: doParallel (>= 1.0) License: AGPL-3 Package: pickgene Version: 1.28.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) Package: PICS Version: 1.10.0 Depends: R (>= 2.11.0), BiocGenerics (>= 0.1.3), IRanges (>= 1.13.10), GenomicRanges, BSgenome Imports: methods, BiocGenerics, stats4, IRanges, GenomicRanges, BSgenome, graphics, grDevices, stats Suggests: snowfall, ShortRead, rtracklayer Enhances: multicore License: Artistic-2.0 Archs: i386, x64 Package: PING Version: 1.0.0 Depends: R(>= 2.11.0),chipseq Imports: methods, graphics, grDevices, stats, GenomeGraphs, fda , IRanges, GenomicRanges, BSgenome, stats4, BiocGenerics Suggests: snowfall, ShortRead, rtracklayer Enhances: parallel License: Artistic-2.0 Archs: i386, x64 Package: pint Version: 1.8.0 Depends: mvtnorm, methods, graphics, Matrix, dmt License: FreeBSD Package: pkgDepTools Version: 1.22.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl, BiocInstaller License: GPL-2 Package: plateCore Version: 1.14.0 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: 1.28.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), MASS Imports: utils License: GPL-2 Package: plier Version: 1.26.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) Archs: i386, x64 Package: PLPE Version: 1.16.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) Package: plw Version: 1.16.0 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: 1.22.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.6) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable License: Artistic-2.0 Package: prada Version: 1.32.0 Depends: R (>= 2.10.0), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, BiocGenerics, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, stats4, utils Suggests: cellHTS, tcltk License: LGPL Archs: i386, x64 Package: PREDA Version: 1.2.0 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: 1.18.0 Depends: methods Imports: stats License: LGPL (>= 2) Archs: i386, x64 Package: PROcess Version: 1.32.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 Package: procoil Version: 1.6.0 Depends: R (>= 2.10.1), methods Imports: methods, stats, graphics, utils Suggests: Biostrings License: GPL (>= 2) Package: PROMISE Version: 1.8.0 Depends: R (>= 2.11.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) Package: puma Version: 2.8.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.23.4), graphics, grDevices, methods, stats, utils, mclust Imports: Biobase (>= 2.5.5), affy (>= 1.23.4) Suggests: pumadata, affydata, snow, limma, annotate, ROCR License: LGPL Archs: i386, x64 Package: pvac Version: 1.4.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) Package: qpcrNorm Version: 1.14.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) Package: qpgraph Version: 1.12.2 Depends: R (>= 2.10), methods Imports: methods, annotate, Matrix, graph, Biobase, GGBase, AnnotationDbi Suggests: Matrix, mvtnorm, graph, genefilter, Category, org.EcK12.eg.db, GOstats Enhances: rlecuyer, snow, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Package: qrqc Version: 1.10.0 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: QUALIFIER Version: 1.0.2 Depends: R (>= 2.14.0),reshape,flowWorkspace, Imports: MASS,hwriter,RSVGTipsDevice,lattice,stats4,flowCore,flowViz,methods Enhances: ncdfFlow License: Artistic-2.0 Package: quantsmooth Version: 1.22.2 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 Package: qvalue Version: 1.30.0 Imports: graphics, grDevices, stats, tcltk License: LGPL Package: r3Cseq Version: 1.2.0 Depends: R (>= 2.14.0), IRanges, BSgenome,ShortRead, rtracklayer, RColorBrewer, methods Suggests: BSgenome.Mmusculus.UCSC.mm9 License: GPL-3 Package: R453Plus1Toolbox Version: 1.6.1 Depends: R (>= 2.12.0), BiocGenerics, Biobase, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer2,TeachingDemos Imports: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), biomaRt, Biostrings, BSgenome, IRanges (>= 1.13.10), methods, R2HTML, Rsamtools, rtracklayer, ShortRead Suggests: rtracklayer, ShortRead, Rsamtools, BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Archs: i386, x64 Package: rama Version: 1.30.0 Depends: R(>= 2.5.0) License: GPL (>= 2) Archs: i386, x64 Package: RamiGO Version: 1.2.0 Depends: gsubfn,methods Imports: igraph,RCurl,png,RCytoscape,graph License: Artistic-2.0 Package: randPack Version: 1.2.0 Depends: methods Imports: Biobase License: Artistic-2.0 Package: RankProd Version: 2.28.0 Depends: R (>= 1.9.0) Imports: graphics License: file LICENSE Package: RbcBook1 Version: 1.24.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 Package: RBGL Version: 1.32.1 Depends: graph, methods Imports: methods Suggests: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Package: RBioinf Version: 1.16.0 Depends: graph, methods License: Artistic-2.0 Archs: i386, x64 Package: rbsurv Version: 2.14.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) Package: RCASPAR Version: 1.2.0 License: GPL (>= 3) Package: RchyOptimyx Version: 1.0.0 Depends: R (>= 2.10) Imports: Rgraphviz, sfsmisc, graphics, methods, graph, grDevices Suggests: flowCore, flowType License: Artistic-2.0 Archs: i386, x64 Package: RCytoscape Version: 1.6.5 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: 1.16.0 Depends: R (>= 2.0.0), RcppClassic, Rcpp LinkingTo: RcppClassic, Rcpp Suggests: RUnit License: GPL-2 Archs: i386, x64 Package: RDRToolbox Version: 1.6.0 Depends: R (>= 2.9.0),rgl Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) Package: ReactomePA Version: 1.0.1 Imports: methods, AnnotationDbi, reactome.db, stats4, plyr, igraph0, qvalue, graphics, org.Hs.eg.db Suggests: clusterProfiler, DOSE, GOSemSim License: GPL-2 Package: ReadqPCR Version: 1.2.0 Depends: R(>= 2.10.0), Biobase, methods, affy Imports: Biobase License: LGPL-3 Package: reb Version: 1.32.0 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) License: GPL-2 Archs: i386, x64 Package: RedeR Version: 1.2.5 Depends: R (>= 2.15), igraph0, RCurl, XML, XMLRPC Imports: rJava, methods Suggests: PANR, HTSanalyzeR, pvclust, graph License: GPL (>= 2) Package: REDseq Version: 1.2.0 Depends: R (>= 2.14.0), 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: 1.26.0 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: 1.2.0 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, DNAcopy, Ringo, aroma.affymetrix Suggests: GenomicRanges, IRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) Package: ReQON Version: 1.3.9 Depends: R (>= 2.15.0), Rsamtools, seqbias Imports: rJava, graphics, stats, utils, grDevices License: GPL-2 Package: Resourcerer Version: 1.30.0 Depends: R (>= 1.9.0), Biobase, AnnotationDbi (>= 1.4.0) Suggests: human.db0, mouse.db0, rat.db0 License: LGPL Package: rGADEM Version: 2.4.0 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: Rgraphviz Version: 1.34.2 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graph, graphics, grDevices, grid, methods, utils License: Artistic-2.0 Archs: i386, x64 Package: rhdf5 Version: 2.0.2 Depends: methods Imports: zlibbioc License: Artistic-2.0 Archs: i386, x64 Package: rHVDM Version: 1.22.0 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: 1.20.0 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: RLMM Version: 1.18.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) Package: Rmagpie Version: 1.12.0 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: 1.6.0 Depends: methods Suggests: RCurl License: Artistic-2.0 Package: RmiR Version: 1.12.0 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: 1.4.0 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: 2.4.0 Depends: R (>= 2.10), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt, car, splots, methods License: Artistic-2.0 Package: ROC Version: 1.32.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase License: Artistic-2.0 Archs: i386, x64 Package: Rolexa Version: 1.12.0 Depends: R (>= 2.9.0), graphics, grDevices, methods, ShortRead Imports: mclust, Biostrings, graphics, grDevices, IRanges, methods, ShortRead, stats Enhances: fork License: GPL-2 Package: RPA Version: 1.12.0 Depends: R (>= 2.14.1), affy, affydata, methods, parallel License: FreeBSD Package: RpsiXML Version: 1.16.0 Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2), AnnotationDbi Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI License: LGPL-3 Package: rqubic Version: 1.2.0 Depends: methods, Biobase, biclust Imports: Biobase, biclust Suggests: RColorBrewer License: GPL-2 Archs: i386, x64 Package: Rsamtools Version: 1.8.6 Depends: methods, IRanges (>= 1.13.30), GenomicRanges (>= 1.7.43), Biostrings (>= 2.21.12) Imports: methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc, bitops, BiocGenerics (>= 0.1.3) LinkingTo: Biostrings, IRanges Suggests: ShortRead (>= 1.13.19), GenomicFeatures, RUnit, KEGG.db License: Artistic-2.0 + file LICENSE Archs: i386, x64 Package: rsbml Version: 2.14.4 Depends: R (>= 2.6.0), methods, utils Imports: graph, utils License: Artistic-2.0 Archs: i386, x64 Package: RTCA Version: 1.8.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 Package: RTopper Version: 1.2.0 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.db License: GPL (>= 3) Package: rtracklayer Version: 1.16.3 Depends: R (>= 2.10), methods, GenomicRanges Imports: XML (>= 1.98-0), BiocGenerics (>= 0.1.0), IRanges (>= 1.13.14), GenomicRanges (>= 1.7.28), Biostrings (>= 2.23.2), 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: 1.18.0 Depends: R (>= 2.5.0), methods, graph, Biobase Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL Archs: i386, x64 Package: safe Version: 2.16.0 Depends: R (>= 2.4.0), Biobase, annotate, methods Imports: SparseM, GO.db, annotate, AnnotationDbi, survival, Biobase Suggests: GO.db, GOstats, Rgraphviz, multtest, hu6800.db, survival License: GPL (>= 2) Package: sagenhaft Version: 1.26.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, methods, SparseM, stats, utils License: GPL (>= 2) Package: SAGx Version: 1.30.0 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: 1.10.0 Depends: R (>= 2.10) Imports: methods License: GPL (>= 2) Archs: i386, x64 Package: SBMLR Version: 1.52.0 Depends: XML, deSolve License: GPL-2 Package: ScISI Version: 1.28.0 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: 1.8.0 Depends: R (>= 2.3.0), methods, baySeq (>= 1.8.1), ShortRead, GenomicRanges, IRanges Imports: baySeq, graphics, grDevices, IRanges, methods, utils, GenomicRanges Suggests: snow License: GPL-3 Package: seqbias Version: 1.4.0 Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods Imports: zlibbioc LinkingTo: Rsamtools Suggests: Rsamtools, ggplot2 License: LGPL-3 Archs: i386, x64 Package: seqLogo Version: 1.22.0 Depends: methods, grid License: LGPL (>= 2) Package: ShortRead Version: 1.14.4 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.4), GenomicRanges (>= 1.7.43), Biostrings (>= 2.23.2), lattice, Rsamtools (>= 1.7.42), latticeExtra Imports: BiocGenerics, IRanges, GenomicRanges, Biostrings, Biobase, hwriter, Rsamtools, zlibbioc, lattice LinkingTo: IRanges, Biostrings Suggests: biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi Enhances: Rmpi, parallel License: Artistic-2.0 Archs: i386, x64 Package: sigaR Version: 1.0.0 Depends: Biobase, CGHbase, corpcor (>= 1.6.2), methods Imports: graphics, marray, MASS, mvtnorm, quadprog, snowfall, stats License: GPL (>= 2) Package: siggenes Version: 1.30.0 Depends: methods, Biobase, multtest, splines, graphics Imports: stats4 Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5) License: LGPL (>= 2) Package: sigPathway Version: 1.24.0 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: 1.26.0 Depends: R (>= 2.4), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt License: GPL (>= 2) Archs: i386, x64 Package: simpleaffy Version: 2.32.0 Depends: R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6), genefilter, gcrma Imports: methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma License: GPL (>= 2) Archs: i386, x64 Package: sizepower Version: 1.26.0 Depends: stats License: LGPL Package: SLGI Version: 1.16.0 Depends: R (>= 2.10), ScISI, lattice Imports: AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice, methods, stats, BiocGenerics Suggests: GO.db, org.Sc.sgd.db License: Artistic-2.0 Package: SLqPCR Version: 1.22.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) Package: SMAP Version: 1.20.0 Depends: R (>= 2.10), methods License: GPL-2 Archs: i386, x64 Package: snapCGH Version: 1.26.0 Depends: limma, DNAcopy, methods Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils License: GPL Archs: i386, x64 Package: snm Version: 1.4.0 Depends: R(>= 2.12.0), lme4, splines, corpcor License: LGPL Package: SNPchip Version: 2.2.0 Depends: R (>= 2.14.0) Imports: graphics, lattice, grid, foreach, IRanges, utils, methods, oligoClasses (>= 1.17.25), Biobase Suggests: crlmm Enhances: doSNOW, VanillaICE, RColorBrewer License: LGPL (>= 2) Package: snpStats Version: 1.6.0 Depends: R(>= 2.10.0), survival, methods, Matrix Imports: graphics, grDevices, methods, stats, survival, utils, Matrix Suggests: hexbin License: GPL-3 Archs: i386, x64 Package: spade Version: 1.2.0 Depends: R (>= 2.11), igraph Imports: Biobase, flowCore Suggests: flowViz License: GPL-2 Archs: i386, x64 Package: SpeCond Version: 1.10.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) Package: SPIA Version: 2.6.0 Depends: R (>= 2.10), graphics Imports: graphics Suggests: graph, Rgraphviz, KEGGgraph, hgu133plus2.db License: GPL (>= 2) Package: spikeLI Version: 2.16.0 Imports: graphics, grDevices, stats, utils License: GPL-2 Package: spkTools Version: 1.12.0 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: 1.28.0 Depends: R (>= 2.6.0), methods, Biobase(>= 2.5.5) Imports: annotate, Biobase, graphics, grDevices, grid, methods, utils, XML License: LGPL Package: splots Version: 1.22.0 Imports: grid, RColorBrewer License: LGPL Package: spotSegmentation Version: 1.30.0 Depends: R (>= 2.10), mclust License: GPL (>= 2) Package: SQUADD Version: 1.6.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>= 2) Package: SRAdb Version: 1.10.0 Depends: RSQLite (>= 0.8-4) , graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 Package: sscore Version: 1.28.0 Depends: R (>= 1.8.0), affy, affyio Suggests: affydata License: GPL (>= 2) Package: ssize Version: 1.30.2 Depends: gdata, xtable License: LGPL Package: SSPA Version: 1.12.0 Depends: R (>= 2.8), methods, qvalue Imports: graphics, limma, methods, stats Suggests: multtest, quadprog, splines License: GPL (>= 2) Package: Starr Version: 1.12.0 Depends: Ringo, affy, affxparser Imports: pspline, MASS, zlibbioc License: Artistic-2.0 Archs: i386, x64 Package: stepNorm Version: 1.28.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL Package: stepwiseCM Version: 1.2.1 Depends: R (>= 2.14), randomForest, MAclinical, tspair, pamr, snowfall, glmpath, penalized, e1071 License: GPL Package: Streamer Version: 1.2.1 Imports: methods, graph Suggests: RUnit, Rsamtools (>= 1.5.53) Enhances: multicore License: Artistic-2.0 Archs: i386, x64 Package: survcomp Version: 1.6.0 Depends: R (>= 2.10), survival, prodlim Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta Suggests: Hmisc, CPE, clinfun, survJamda, Biobase License: Artistic-2.0 Archs: i386, x64 Package: sva Version: 3.2.1 Depends: R (>= 2.8), corpcor, mgcv Suggests: limma,pamr,bladderbatch License: Artistic-2.0 Archs: i386, x64 Package: TargetSearch Version: 1.12.3 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: 1.6.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 Package: TEQC Version: 2.4.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) Package: ternarynet Version: 1.0.0 Depends: R (>= 2.10.0), methods License: GPL (>= 2) Archs: i386, x64 Package: tigre Version: 1.10.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, BiocGenerics, Biobase, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite Suggests: puma, drosgenome1.db, annotate, lumi License: AGPL-3 Archs: i386, x64 Package: tilingArray Version: 1.34.0 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: 1.28.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL Package: tkWidgets Version: 1.34.0 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: 2.8.0 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: trigger Version: 1.2.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 Archs: i386, x64 Package: tspair Version: 1.14.1 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 Archs: i386, x64 Package: TSSi Version: 1.2.0 Depends: R (>= 2.13.2) Imports: methods, Hmisc, minqa, stats, Biobase, plyr, IRanges Suggests: rtracklayer Enhances: multicore License: GPL-3 Archs: i386, x64 Package: TurboNorm Version: 1.4.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: affydata, affy, lattice License: LGPL Package: tweeDEseq Version: 1.2.1 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) Archs: i386, x64 Package: twilight Version: 1.32.0 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: 1.22.0 Depends: methods Suggests: Biobase License: BSD Package: VanillaICE Version: 1.18.0 Depends: R (>= 2.14.0) Imports: stats, utils, methods, Biobase, oligoClasses (>= 1.17.36), lattice, IRanges (>= 1.13.22), grid, msm, crlmm (>= 1.13.12), foreach Suggests: genomewidesnp6Crlmm, hapmapsnp6, RColorBrewer, genefilter, RSQLite, foreach, RUnit, pd.mapping50k.hind240, SNPchip (>= 2.0.3) Enhances: DNAcopy, crlmm License: LGPL-2 Archs: i386, x64 Package: VariantAnnotation Version: 1.2.11 Depends: R (>= 2.8.0), methods, GenomicRanges (>= 1.8.13), Rsamtools (>= 1.7.41) Imports: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Biobase (>= 2.15.1), Rsamtools (>= 1.7.41), AnnotationDbi (>= 1.17.11), Biostrings (>= 2.23.4), zlibbioc, BSgenome, GenomicFeatures, snpStats, DBI LinkingTo: IRanges, Biostrings, Rsamtools Suggests: RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131 License: Artistic-2.0 Archs: i386, x64 Package: vbmp Version: 1.24.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) Package: Vega Version: 1.4.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: VegaMC Version: 2.0.0 Depends: R (>= 2.10.0), biomaRt, Biobase, genoset Imports: methods License: GPL-2 Archs: i386, x64 Package: virtualArray Version: 1.0.0 Depends: R (>= 2.3.0), methods, plyr, preprocessCore Imports: affy, affyPLM, AnnotationDbi, Biobase, gcrma, GEOquery, graphics, methods, reshape2, stats, utils Suggests: affydata, plier, limma, lumi, org.Hs.eg.db Enhances: multicore License: GPL-3 Package: vsn Version: 3.24.0 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: weaver Version: 1.22.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 Package: webbioc Version: 1.28.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: Biobase, multtest, qvalue, stats, utils License: GPL (>= 2) Package: widgetTools Version: 1.34.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL Package: xcms Version: 1.32.0 Depends: R (>= 1.9.0), methods, mzR (>= 1.1.6) Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>= 1.5.2), RANN, snow, RUnit Enhances: Rgraphviz, XML, KEGGSOAP License: GPL (>= 2) Archs: i386, x64 Package: XDE Version: 2.2.0 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 Enhances: coda License: LGPL-2 Archs: i386, x64 Package: xmapbridge Version: 1.14.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 Package: yaqcaffy Version: 1.16.1 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 Package: zlibbioc Version: 1.2.0 License: Artistic-2.0 + file LICENSE Archs: i386, x64