Package: a4 Version: 1.12.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo License: GPL-3 MD5sum: d40e5248bd26b817b36e78ecbe3351dd NeedsCompilation: no Package: a4Base Version: 1.12.0 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: c5e70813cb82c0725c68c7a97b202142 NeedsCompilation: no Package: a4Classif Version: 1.12.0 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL License: GPL-3 MD5sum: 55dfad638644d6ee70ca7d3c9e3df346 NeedsCompilation: no Package: a4Core Version: 1.12.0 Depends: methods, Biobase, glmnet License: GPL-3 MD5sum: 3c415b2dfc7667c30815047cb3ece4f9 NeedsCompilation: no Package: a4Preproc Version: 1.12.0 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 MD5sum: 1e7c4fd08f2de55ec95fb4dda9a974be NeedsCompilation: no Package: a4Reporting Version: 1.12.0 Depends: methods, annaffy Imports: xtable, utils License: GPL-3 MD5sum: d8decf685f92393f2948e1674c8f247f NeedsCompilation: no Package: ABarray Version: 1.32.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL MD5sum: 9d4f2bfb6dd7be6c1128a4f359c93c3d NeedsCompilation: no Package: ABSSeq Version: 1.0.1 Depends: R (>= 2.10), methods Imports: Rcpp LinkingTo: Rcpp License: GPL (>= 3) MD5sum: 59b203b19932d2b2352c1a55bb756151 NeedsCompilation: yes Package: aCGH Version: 1.42.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, cluster, grDevices, graphics, methods, multtest, stats, survival, splines, utils License: GPL-2 MD5sum: 2d3185ce9535212fc5fb92528347d194 NeedsCompilation: yes Package: ACME Version: 2.20.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods Imports: graphics, stats License: GPL (>= 2) MD5sum: 0133d78c91040dfec94e80ff3cf6640e NeedsCompilation: yes Package: ADaCGH2 Version: 2.4.0 Depends: R (>= 2.15.0), parallel, ff Imports: bit, ffbase, DNAcopy, tilingArray, GLAD, waveslim, cluster, aCGH, snapCGH Suggests: CGHregions, Cairo, limma Enhances: Rmpi License: GPL (>= 3) MD5sum: e3d8f3746d3dd9065976ab1ae4bf4e13 NeedsCompilation: yes Package: adSplit Version: 1.34.0 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) MD5sum: ddd955fb91a6d9907a24341e40281d1f NeedsCompilation: yes Package: affxparser Version: 1.36.0 Depends: R (>= 2.6.0) Suggests: R.utils (>= 1.29.8), AffymetrixDataTestFiles License: LGPL (>= 2) MD5sum: 962b5d52adae87e1027b07135085e975 NeedsCompilation: yes Package: affy Version: 1.42.3 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: 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) MD5sum: e9dbe1e70f27fab2378db2266ac473c7 NeedsCompilation: yes Package: affycomp Version: 1.40.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) MD5sum: 120b21b8b8335547c30130c1310b32f1 NeedsCompilation: no Package: AffyCompatible Version: 1.24.1 Depends: R (>= 2.7.0), XML (>= 2.8-1), RCurl (>= 0.8-1), methods Imports: Biostrings License: Artistic-2.0 MD5sum: 3032330233df58ac263609cf1f476979 NeedsCompilation: no Package: affyContam Version: 1.22.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata License: Artistic-2.0 MD5sum: 475d228526821f44365f28962cd2ab13 NeedsCompilation: no Package: affycoretools Version: 1.36.1 Depends: affy, Biobase, GO.db Imports: biomaRt, limma, GOstats, annotate, annaffy, genefilter, gcrma, splines, xtable, AnnotationDbi, lattice, gplots, R2HTML, oligoClasses, ReportingTools, hwriter Suggests: affydata, hgfocuscdf, rgl, BiocStyle, knitr License: Artistic-2.0 MD5sum: eab3e820b940176e1f7378a47468cfe9 NeedsCompilation: no Package: AffyExpress Version: 1.30.0 Depends: R (>= 2.10), affy (>= 1.23.4), limma Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma License: LGPL MD5sum: efd76f30ef400c49b912a58f6708f9bd NeedsCompilation: no Package: affyILM Version: 1.16.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, methods, Biobase Suggests: AffymetrixDataTestFiles License: GPL-3 MD5sum: 18a3237b1c47fcc221a24158e03d3d70 NeedsCompilation: no Package: affyio Version: 1.32.0 Depends: R (>= 2.6.0) Imports: zlibbioc License: LGPL (>= 2) MD5sum: e6e6fe070e62d108461904c0a9b9b737 NeedsCompilation: yes Package: affylmGUI Version: 1.38.0 Depends: limma, tcltk, affy, BiocInstaller, affyio, affy, tkrplot, affyPLM, R2HTML, xtable, gcrma, affyPLM, AnnotationDbi License: LGPL MD5sum: 5ae23cd86e6215feed863adfee44de6f NeedsCompilation: no Package: affyPara Version: 1.24.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0), aplpack (>= 1.1.1), affyio Suggests: affydata Enhances: affy License: GPL-3 MD5sum: 4e3b596ea7c616b5985f0582302f0549 NeedsCompilation: no Package: affypdnn Version: 1.38.0 Depends: R (>= 2.13.0), affy (>= 1.5) Suggests: affydata, hgu95av2probe License: LGPL MD5sum: 056436588b4a9e72b3c9d7750b47f51e NeedsCompilation: no Package: affyPLM Version: 1.40.1 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0), Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1) Imports: BiocGenerics, zlibbioc, graphics, grDevices, methods LinkingTo: preprocessCore Suggests: affydata, MASS License: GPL (>= 2) MD5sum: cd6ceb1c0b88c263bc54c90f741b8fbb NeedsCompilation: yes Package: affyQCReport Version: 1.42.0 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) MD5sum: f81381923a16728fef43afe59c9574a9 NeedsCompilation: no Package: AffyRNADegradation Version: 1.10.0 Depends: R (>= 2.9.0), methods, affy Suggests: AmpAffyExample License: GPL-2 MD5sum: e8ddb7c3cf2044b95b771359957d8927 NeedsCompilation: no Package: AffyTiling Version: 1.22.1 Depends: R (>= 2.6) Imports: affxparser, affy (>= 1.16), stats, utils, preprocessCore License: GPL (>= 2) MD5sum: 4dac7c2f837807f6abd43e3bf5aea3e5 NeedsCompilation: yes Package: AGDEX Version: 1.12.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL (>= 2) MD5sum: fc311880979c4406f5070cb72daf4ad5 NeedsCompilation: no Package: agilp Version: 3.6.0 Depends: R (>= 2.14.0) License: GPL-3 MD5sum: 6cca7b88945acdb07d2f2b56a3696897 NeedsCompilation: no Package: AgiMicroRna Version: 2.14.0 Depends: R (>= 2.10),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 MD5sum: d69cc567992e3856070e4eb5bd629162 NeedsCompilation: no Package: AllelicImbalance Version: 1.2.0 Depends: GenomicAlignments, GenomicRanges, R (>= 3.0.0) Imports: methods, BiocGenerics, IRanges, Biostrings, Rsamtools, GenomicFeatures, AnnotationDbi Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,SNPlocs.Hsapiens.dbSNP.20120608 License: GPL-3 MD5sum: 1d6cea0d4b48453132057ab73f726754 NeedsCompilation: no Package: alsace Version: 1.0.0 Depends: R (>= 2.10), ALS, ptw (>= 1.0.6) Suggests: lattice License: GPL (>= 2) MD5sum: 7c4c5c3ab04b68a2a2d9038d78c7e9bd NeedsCompilation: no Package: altcdfenvs Version: 2.26.0 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) MD5sum: 41254fd73605d81eb0d6c30fc28642c9 NeedsCompilation: no Package: ampliQueso Version: 1.2.0 Depends: R (>= 2.15.0), rnaSeqMap (>= 2.17.1), knitr, rgl, ggplot2, gplots, parallel, doParallel, foreach, VariantAnnotation,genefilter,statmod,xtable Imports: edgeR, DESeq, samr License: GPL-2 MD5sum: 30a4d48956775a298cee8210ca594bf5 NeedsCompilation: no Package: annaffy Version: 1.36.0 Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db Imports: AnnotationDbi (>= 0.1.15) Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: 443a2bd7d54ab5225294cc95baab10e6 NeedsCompilation: no Package: annmap Version: 1.6.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: 85535baf6521033c7246d48a6f8cf0c6 NeedsCompilation: no Package: annotate Version: 1.42.1 Depends: R (>= 2.10), AnnotationDbi (>= 0.1.15) Imports: Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats, methods, XML (>= 0.92-2), BiocGenerics (>= 0.1.13) Suggests: Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.25.10), rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, XML (>= 0.92-2), org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, License: Artistic-2.0 MD5sum: b772f65c2b792e8297a3b233b23f2304 NeedsCompilation: no Package: AnnotationDbi Version: 1.26.1 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.5.4), Biobase (>= 1.17.0), GenomeInfoDb(>= 0.99.17) Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase, IRanges Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, seqnames.db, reactome.db, AnnotationForge, graph, org.TguttataTestingSubset.eg.db, BiocStyle, knitr License: Artistic-2.0 MD5sum: b545c34faf86540d18faacb46aef0fa1 NeedsCompilation: no Package: AnnotationForge Version: 1.6.1 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.1.13), Biobase (>= 1.17.0), AnnotationDbi (>= 1.19.15), org.Hs.eg.db Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), XML, RCurl, hgu95av2.db, human.db0, affy, Homo.sapiens, hom.Hs.inp.db, GO.db, BiocStyle, knitr License: Artistic-2.0 MD5sum: 554e98263800ff11db321231e01b29e2 NeedsCompilation: no Package: AnnotationFuncs Version: 1.14.0 Depends: R (>= 2.7.0), AnnotationDbi Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db License: GPL-2 MD5sum: 4054060855e9b31f0fe4b3dd67f5b181 NeedsCompilation: no Package: AnnotationHub Version: 1.4.0 Depends: IRanges Imports: methods, stats, utils, rjson, BiocGenerics, httr, BiocInstaller (>= 1.11.0), AnnotationDbi, GenomicRanges, interactiveDisplay (>= 1.0.23) Suggests: RUnit, RCurl, Rsamtools License: Artistic-2.0 MD5sum: 9e92963a275f507a6e0885b76a0aadd0 NeedsCompilation: no Package: annotationTools Version: 1.38.0 Imports: Biobase, stats License: GPL MD5sum: f58b1cbc1bbfb5fc5c44b49de41be31c NeedsCompilation: no Package: anota Version: 1.12.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 14a525729ef94974cf33ee993becc955 NeedsCompilation: no Package: antiProfiles Version: 1.4.0 Depends: R (>= 3.0), matrixStats (>= 0.5), methods (>= 2.14), Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: 62ece6721f49ea2e528e16a8f14c401c NeedsCompilation: no Package: apComplex Version: 2.30.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 84e8444bdac1d802f1fd8a66fd174e6e NeedsCompilation: no Package: aroma.light Version: 2.0.0 Depends: R (>= 2.14.0), matrixStats (>= 0.8.14) Imports: R.methodsS3 (>= 1.6.1), R.oo (>= 1.18.0) Suggests: R.utils (>= 1.29.8), princurve (>= 1.1-12) License: GPL (>= 2) MD5sum: ab88ff1a6b9d146b786dd5ac7037ac47 NeedsCompilation: no Package: ArrayExpress Version: 1.24.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, affy, limma License: Artistic-2.0 MD5sum: a31431a506fca555ed23e0d36516366b NeedsCompilation: no Package: ArrayExpressHTS Version: 1.14.0 Depends: sampling, Rsamtools (>= 1.3.32), snow Imports: Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges, R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils, sendmailR, bitops LinkingTo: Rsamtools License: Artistic License 2.0 MD5sum: ad6ea9809ffcc28aebd49aa91cad43cb NeedsCompilation: yes Package: arrayMvout Version: 1.22.0 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 MD5sum: a5f605cc6b68ad4b8b803b12e0c110ff NeedsCompilation: no Package: arrayQuality Version: 1.42.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: b55bca21ba9fbb9f581bfd0457b9ded1 NeedsCompilation: no Package: arrayQualityMetrics Version: 3.20.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, Cairo (>= 1.4-6), genefilter, graphics, grDevices, grid, gridSVG, Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, SVGAnnotation (>= 0.9-0), utils, vsn (>= 3.23.3), XML Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 9fa5dda756ca31e8ee88f9f8ec23ca1a NeedsCompilation: no Package: ArrayTools Version: 1.24.0 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) MD5sum: 68301cbca67a5ef64687afd415475303 NeedsCompilation: no Package: ArrayTV Version: 1.2.0 Depends: R (>= 2.14) Imports: foreach, DNAcopy, methods, oligoClasses (>= 1.21.3) Suggests: RColorBrewer, crlmm, ff, BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19, lattice, latticeExtra, RUnit, BiocGenerics Enhances: doMC, doSNOW, doParallel License: GPL (>= 2) MD5sum: 9e413984bd302cbc8d78d9c5587357b6 NeedsCompilation: no Package: ARRmNormalization Version: 1.4.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: 36ca5059f4a8fe1629c7e7c333e3f49e NeedsCompilation: no Package: ASEB Version: 1.8.1 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 239d740699ad2d3074576ec04c863bfb NeedsCompilation: yes Package: asmn Version: 1.0.0 Depends: R (>= 3.0.2) Imports: methylumi, stats, Biobase Suggests: TCGAMethylation450k, IlluminaHumanMethylation450k.db License: GPL-3 MD5sum: 96487834b418e12335cc2515c8abe3f1 NeedsCompilation: no Package: ASSET Version: 1.2.0 Depends: MASS, msm, rmeta Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 4761c40ec41b6208d7a64c42b81b32c8 NeedsCompilation: no Package: ASSIGN Version: 1.0.0 Depends: Rlab, msm, gplots Imports: graphics, grDevices, stats, utils License: MIT MD5sum: a1b84b80903034b4af85d891219f2697 NeedsCompilation: no Package: AtlasRDF Version: 1.0.0 Depends: R (>= 2.10), hash, SPARQL, methods License: Apache License 2.0 MD5sum: 1281c90baa4c00f62212eedb2a614e03 NeedsCompilation: no Package: attract Version: 1.16.0 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) MD5sum: b40a084440cfd31fb8c7ba0d8cf929be NeedsCompilation: no Package: BAC Version: 1.24.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: fa067de427b9b404623081c43651ddb9 NeedsCompilation: yes Package: BADER Version: 1.2.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 1bd107c0ac38679d55faf21f435a3424 NeedsCompilation: yes Package: BAGS Version: 2.4.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: 0962740b95b0733a69fa39890065777e NeedsCompilation: yes Package: BaseSpaceR Version: 1.8.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 097088390af1f01583ee67bee859d54d NeedsCompilation: no Package: Basic4Cseq Version: 1.0.2 Depends: R (>= 3.0.0), Biostrings, ShortRead, caTools, GenomicRanges Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 943eda6304f5a6f10046a5c1a42c859a NeedsCompilation: no Package: BayesPeak Version: 1.16.0 Depends: R (>= 2.14), IRanges Imports: IRanges, graphics Suggests: BiocStyle License: GPL (>= 2) MD5sum: f0eea9bff8476acae8c6443e31fdafcb NeedsCompilation: yes Package: baySeq Version: 1.18.0 Depends: R (>= 2.3.0), methods, GenomicRanges Suggests: snow, edgeR License: GPL-3 MD5sum: 24f82d1b6234e0145887a6748c56c71c NeedsCompilation: no Package: BCRANK Version: 1.26.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: 82fe8a926186573a6022be8741ef53eb NeedsCompilation: yes Package: beadarray Version: 2.14.1 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), methods, ggplot2 Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: GPL-2 MD5sum: 798cadef4221d19195dab23957a276bc NeedsCompilation: yes Package: beadarraySNP Version: 1.30.0 Depends: methods, Biobase (>= 2.5.5), quantsmooth Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy License: GPL-2 MD5sum: 8c672233e176c9e01a314ad0e6153e9e NeedsCompilation: no Package: BeadDataPackR Version: 1.16.0 License: GPL-2 MD5sum: 11e8249d15838811a2f6d4855029b1b5 NeedsCompilation: yes Package: BEAT Version: 1.2.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: 542c203c132ab2dd4386dcb03304fb16 NeedsCompilation: no Package: betr Version: 1.20.0 Depends: R(>= 2.6.0) Imports: Biobase (>= 2.5.5), limma, mvtnorm, methods, stats Suggests: Biobase License: LGPL MD5sum: 8b4b927d51647b171e36a7ae4b6dc546 NeedsCompilation: no Package: bgafun Version: 1.26.0 Depends: made4, seqinr,ade4 License: Artistic-2.0 MD5sum: 86f7dc6078c4e35f78f2c1bd926e85bb NeedsCompilation: no Package: BGmix Version: 1.24.0 Depends: R (>= 2.3.1), KernSmooth License: GPL-2 MD5sum: 19dd57ac8d7f81bed60b3604efdeb936 NeedsCompilation: yes Package: bgx Version: 1.30.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Suggests: affydata, hgu95av2cdf License: GPL-2 MD5sum: 505446ea8a8ae86c6b1eb5152b71e72a NeedsCompilation: yes Package: BHC Version: 1.16.0 License: GPL-3 MD5sum: 2f300b519f9ba6c2361049863306950b NeedsCompilation: yes Package: BicARE Version: 1.22.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase License: GPL-2 MD5sum: b77fa255f4d26319fefd74b26e4f3b60 NeedsCompilation: yes Package: BiGGR Version: 1.2.0 Depends: R (>= 2.14.0), rsbml, hyperdraw, LIM Imports: hypergraph License: file LICENSE MD5sum: 57ea5a89c76647da0718835356c697dc NeedsCompilation: no Package: bigmemoryExtras Version: 1.8.0 Depends: R (>= 2.12), bigmemory (>= 4.3) Imports: bigmemory, biganalytics, methods, BiocGenerics, Biobase Suggests: RUnit, BiocGenerics (>= 0.1.0) License: Artistic-2.0 OS_type: unix MD5sum: 59041a1b943a00beb613d138592c8eb4 NeedsCompilation: no Package: bioassayR Version: 1.2.0 Depends: R (>= 3.0.1), DBI, RSQLite, methods Imports: XML Suggests: BiocStyle, RCurl, ape, ChemmineR License: Artistic-2.0 MD5sum: 16bd0bfc304b65891833686abd6677ac NeedsCompilation: no Package: Biobase Version: 2.24.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets License: Artistic-2.0 MD5sum: 76d14ec2ecba9bc90433998538fa9f83 NeedsCompilation: yes Package: BiocCaseStudies Version: 1.26.0 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 MD5sum: 860c3024867c8c193e4853705ec187ea NeedsCompilation: no Package: BiocCheck Version: 1.0.2 Depends: R (>= 3.1.0) Imports: biocViews (>= 1.31.9), BiocInstaller, graph, devtools (>= 1.4.1), httr, knitr, tools, optparse, codetools, methods Suggests: RUnit, BiocGenerics, Biobase, RJSONIO, knitrBootstrap Enhances: codetoolsBioC License: Artistic-2.0 MD5sum: 21a9272651e6f1be626e1e9c5da95c6e NeedsCompilation: no Package: BiocGenerics Version: 0.10.0 Depends: methods, utils, graphics, stats, parallel Imports: methods, utils, graphics, stats, parallel Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy, RUnit, DESeq2 License: Artistic-2.0 MD5sum: 431e30b3dee2add008b552c6598e1ead NeedsCompilation: no Package: biocGraph Version: 1.26.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 MD5sum: f4b0deb14a00c762364fae69d194c631 NeedsCompilation: no Package: BiocInstaller Version: 1.14.3 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 1bcf919334a89dbd67e0c60707780a06 NeedsCompilation: no Package: BiocParallel Version: 0.6.1 Imports: methods, parallel, foreach, tools, BatchJobs, BBmisc, BiocGenerics Suggests: doParallel, snow, Rmpi, RUnit, BiocStyle, knitr License: GPL-2 | GPL-3 MD5sum: c3bda325c9136eadc138bbf0b951af2c NeedsCompilation: no Package: BiocStyle Version: 1.2.0 Suggests: knitr, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 178320cf980369efe9617e6a758c67e5 NeedsCompilation: no Package: biocViews Version: 1.32.1 Depends: R (>= 2.4.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, knitr Suggests: Biobase License: Artistic-2.0 MD5sum: 9bd5bf6b9d440cf9029001c67e018a2c NeedsCompilation: no Package: bioDist Version: 1.36.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 MD5sum: 8ef8a957e42051da61b6b95f62a12c3b NeedsCompilation: no Package: biomaRt Version: 2.20.0 Depends: methods Imports: utils, XML, RCurl, AnnotationDbi Suggests: annotate License: Artistic-2.0 MD5sum: ad5e7c7b1d28ef5396838ae223b264ed NeedsCompilation: no Package: BioMVCClass Version: 1.32.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL MD5sum: 431c84d9c5358c0cf73f9b5d5c4e0444 NeedsCompilation: no Package: biomvRCNS Version: 1.4.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 2965a79c98141e72c6f9d3c83db7b11a NeedsCompilation: yes Package: BioNet Version: 1.24.1 Depends: R (>= 2.10.0), Biobase, graph, RBGL Imports: igraph (>= 0.7), AnnotationDbi Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) MD5sum: 56e8b102902a1b406e28ed924183f07f NeedsCompilation: no Package: BioSeqClass Version: 1.22.0 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) MD5sum: b257d005150304aab84d9b9894c802fe NeedsCompilation: no Package: Biostrings Version: 2.32.1 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.5.4), IRanges (>= 1.21.35), XVector (>= 0.3.6) Imports: graphics, methods, stats, utils, BiocGenerics, IRanges, XVector, zlibbioc LinkingTo: IRanges, XVector Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit Enhances: Rmpi License: Artistic-2.0 MD5sum: eaaf4742709dcae91caa7966a696f5fe NeedsCompilation: yes Package: biosvd Version: 1.0.0 Depends: R (>= 3.0.0) Imports: gplots, BiocGenerics, Biobase, methods, grid, hwriter, ReportingTools, graphics License: Artistic-2.0 MD5sum: c7f8434cbdb62e45f3a20db16aa559db NeedsCompilation: no Package: biovizBase Version: 1.12.3 Depends: R (>= 2.10), methods Imports: methods, grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, IRanges, GenomicRanges (>= 1.13.3), Biostrings, Rsamtools (>= 1.13.1), GenomicAlignments, GenomicFeatures, AnnotationDbi, VariantAnnotation Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer License: Artistic-2.0 MD5sum: 38c3862b0a4f3b7255220d58f2e59c1f NeedsCompilation: yes Package: BiRewire Version: 1.6.5 Depends: igraph Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 94b2c3d5dcd0846daaeb67f7d04cd415 NeedsCompilation: yes Package: birta Version: 1.8.0 Depends: limma, MASS, R(>= 2.10), Biobase, methods License: GPL (>= 2) MD5sum: f4e38d2b3cf8125f12e12059f41eb3b0 NeedsCompilation: yes Package: BiSeq Version: 1.4.2 Depends: R (>= 2.15.2), methods, IRanges (>= 1.17.24), GenomicRanges, Formula Imports: methods, BiocGenerics, Biobase, IRanges, GenomicRanges, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 MD5sum: 3cb9af6e3b9adb4a618ce5c63e8fcf16 NeedsCompilation: no Package: BitSeq Version: 1.8.0 Depends: Rsamtools, zlibbioc Imports: IRanges LinkingTo: Rsamtools, zlibbioc Suggests: edgeR, DESeq License: Artistic-2.0 + file LICENSE MD5sum: e2e041f1949775738c732a60dfbebc1d NeedsCompilation: yes Package: BRAIN Version: 1.10.1 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: cdbe172993da16f7d96103d8f798ed07 NeedsCompilation: no Package: BrainStars Version: 1.8.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 MD5sum: b5a1a37bc86da506da5924c31e677d91 NeedsCompilation: no Package: bridge Version: 1.28.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) MD5sum: ca2fbbaf31d72656b722f3335a007132 NeedsCompilation: yes Package: BSgenome Version: 1.32.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>= 1.13.6), GenomicRanges (>= 1.15.9), Biostrings (>= 2.23.3) Imports: methods, BiocGenerics, IRanges, GenomicRanges, XVector, Biostrings, Rsamtools Suggests: BiocInstaller, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19.masked, SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase, GenomeInfoDb, RUnit License: Artistic-2.0 MD5sum: ed71b9d8b23ea959e29487f6bd688e41 NeedsCompilation: no Package: bsseq Version: 1.0.0 Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, parallel, matrixStats Imports: scales, stats, graphics, Biobase, locfit Suggests: RUnit, bsseqData License: Artistic-2.0 MD5sum: 6dd6ca0dcbc603503655981bbcec4d7c NeedsCompilation: no Package: BufferedMatrix Version: 1.28.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: 53e92954768ef94395a152dcc2b1c6a5 NeedsCompilation: yes Package: BufferedMatrixMethods Version: 1.28.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) MD5sum: 67b8c355750e35c6ee507cd36bb5248d NeedsCompilation: yes Package: bumphunter Version: 1.4.2 Depends: R (>= 2.10), IRanges, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils Suggests: RUnit, BiocGenerics, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: be66ffbeabfbdeccda9b8d0f31eff06f NeedsCompilation: no Package: BUS Version: 1.20.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: db4b54b388e72220c23c365391d737e9 NeedsCompilation: yes Package: CAFE Version: 1.0.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 5c5332085d6d21508e82c9dc2ac00de9 NeedsCompilation: no Package: CAGEr Version: 1.6.1 Depends: methods, R (>= 2.15.0), BSgenome Imports: Rsamtools, GenomicRanges, IRanges, data.table, beanplot, rtracklayer, som, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, FANTOM3and4CAGE Enhances: parallel License: GPL-3 MD5sum: cdd6cadb628495c7451d679004bc9268 NeedsCompilation: no Package: CALIB Version: 1.30.0 Depends: R (>= 2.10), limma, methods Imports: limma, methods, graphics, stats, utils License: LGPL MD5sum: 302065a505e87241ccd002214f4a33de NeedsCompilation: yes Package: CAMERA Version: 1.20.0 Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5), igraph Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 03c0613339814dd9b707a9a12b424f10 NeedsCompilation: yes Package: cancerclass Version: 1.8.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 62ce4046506899fa9c94ac54f2dc2a73 NeedsCompilation: yes Package: CancerMutationAnalysis Version: 1.8.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE MD5sum: 361bef79df30357a32d6e1341691bc29 NeedsCompilation: yes Package: casper Version: 1.9.0 Depends: R (>= 2.14.1), Biobase, IRanges, methods, GenomicRanges Imports: BiocGenerics, EBarrays, gaga, gtools, GenomicFeatures, mgcv, Rsamtools, rtracklayer, sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) MD5sum: d8f26bb4428ccf13b720347f6b993443 NeedsCompilation: yes Package: Category Version: 2.30.0 Depends: BiocGenerics, AnnotationDbi, Biobase, Matrix, GO.db, methods Imports: BiocGenerics, graph, methods, Biobase, AnnotationDbi, RBGL, GSEABase (>= 1.19.3), genefilter, annotate (>= 1.15.6), stats, utils Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGG.db, SNPchip, geneplotter, limma, lattice, graph, Biobase, genefilter, methods, RUnit, org.Sc.sgd.db, GOstats License: Artistic-2.0 MD5sum: d9d5eef63a165aa9c6f2c1cf9c6fadba NeedsCompilation: no Package: categoryCompare Version: 1.8.0 Depends: R (>= 2.10), Biobase, BiocGenerics Imports: AnnotationDbi, hwriter, GSEABase, Category, GOstats, annotate, colorspace, graph, RCytoscape (>= 1.5.11) Suggests: methods, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter License: GPL-2 MD5sum: 36577cd91e6da83f59edda5bbed0ba7e NeedsCompilation: no Package: ccrepe Version: 1.0.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics License: MIT + file LICENSE MD5sum: 41f054a76b6fbe9031eb977afab40f7d NeedsCompilation: no Package: cellGrowth Version: 1.8.0 Depends: R (>= 2.12.0), locfit (>= 1.5-4) Imports: lattice License: Artistic-2.0 MD5sum: 8c70fb31553088c16f054e781d9f706a NeedsCompilation: no Package: cellHTS Version: 1.34.0 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 MD5sum: 5e60aa3733221ea53ba1d65cb4080874 NeedsCompilation: no Package: cellHTS2 Version: 2.28.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: prada, GSEABase, Category, stats4 License: Artistic-2.0 MD5sum: a776de45023278eba463df20618ae8c3 NeedsCompilation: no Package: CellNOptR Version: 1.10.0 Depends: R (>= 2.15.0), RBGL, graph, methods, hash, ggplot2, RCurl, Rgraphviz, XML Suggests: RUnit, BiocGenerics, igraph License: GPL-3 MD5sum: f1fba7425bdd02d192d8ee260832142b NeedsCompilation: yes Package: CexoR Version: 1.2.0 Depends: R (>= 2.10.0), IRanges Imports: Rsamtools, GenomicRanges, rtracklayer, idr Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: 1c48ebec4b5042f76c975ef1aa87a0a4 NeedsCompilation: no Package: CGEN Version: 2.6.1 Depends: R (>= 2.10.1), survival Suggests: cluster License: GPL-2 + file LICENSE MD5sum: a596c1e3fd303a6a4ef24b805a4d975c NeedsCompilation: yes Package: CGHbase Version: 1.24.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: e4cadbd9c3ea21c88aebcba7b1c1e432 NeedsCompilation: no Package: CGHcall Version: 2.26.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall License: GPL MD5sum: cfdbbcb1293108e84560b937a54fc382 NeedsCompilation: no Package: cghMCR Version: 1.22.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 4bc6a1875219b0218999ddf260c28365 NeedsCompilation: no Package: CGHnormaliter Version: 1.18.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: 9beee3216314bfad1ead2ad3e414542a NeedsCompilation: no Package: CGHregions Version: 1.22.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase License: GPL MD5sum: d14c06d03dd279d8c1ad075bfe70efb5 NeedsCompilation: no Package: ChAMP Version: 1.2.8 Depends: R (>= 3.0.1), minfi, ChAMPdata, Illumina450ProbeVariants.db Imports: sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr License: GPL-3 MD5sum: 0608e334e91b291ab6099467ab66cd00 NeedsCompilation: no Package: charm Version: 2.10.1 Depends: R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter Imports: BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses(>= 1.17.39), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils, limma, parallel, sva(>= 3.1.2) Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor License: LGPL (>= 2) MD5sum: b1ec8d554217d7d3cafd8c6ae5e8e6ef NeedsCompilation: no Package: ChemmineOB Version: 1.2.9 Depends: R (>= 2.15.1), methods Imports: BiocGenerics, zlibbioc LinkingTo: BH Suggests: ChemmineR, BiocStyle,knitr,knitcitations Enhances: ChemmineR (>= 2.13.0) License: file LICENSE MD5sum: 0252ad63c02f4edbef42cc5e98c86f62 NeedsCompilation: yes Package: ChemmineR Version: 2.16.9 Depends: R (>= 2.10.0), methods Imports: graphics, methods, stats, RCurl, DBI, digest, BiocGenerics Suggests: RSQLite, scatterplot3d, gplots, fmcsR,snow, RPostgreSQL, BiocStyle,knitr,knitcitations, ChemmineOB Enhances: ChemmineOB License: Artistic-2.0 MD5sum: 9987be638add7562bce496311347f655 NeedsCompilation: yes Package: chimera Version: 1.6.16 Depends: Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1), GenomicAlignments, methods, AnnotationDbi, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: BiocParallel Enhances: Rsubread, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db License: Artistic-2.0 MD5sum: 3c168175b78d335a1fa20439fed39d82 NeedsCompilation: no Package: chipenrich Version: 1.2.0 Depends: R (>= 2.15.1) Imports: chipenrich.data, methods, GenomicRanges (>= 1.10.0), IRanges (>= 1.16.0), mgcv, plyr (>= 1.7.0), lattice, latticeExtra, grid, stringr (>= 0.6), reshape License: GPL-3 MD5sum: 0ee579208398d60f473f15ce990a3bdf NeedsCompilation: no Package: ChIPpeakAnno Version: 2.14.1 Depends: R (>= 2.10), grid,VennDiagram, biomaRt, IRanges, Biostrings Imports: BiocGenerics (>= 0.1.0), GO.db, BSgenome, GenomicFeatures, AnnotationDbi, limma, multtest Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, org.Hs.eg.db, gplots, RUnit License: GPL (>= 2) MD5sum: ecab1c86e2c12d987e7a758391513066 NeedsCompilation: no Package: ChIPQC Version: 1.0.9 Depends: R (>= 3.0.0), ggplot2, DiffBind Imports: BiocGenerics (>= 0.8.0), Rsamtools (>= 1.14.2), GenomicRanges (>= 1.14.4), chipseq (>= 1.12.0), GenomicAlignments (>= 0.99.2), gtools, BiocParallel, methods, IRanges, reshape2, Nozzle.R1, Biobase,grDevices, stats, utils Suggests: BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene License: GPL (>= 3) MD5sum: acbf38b61212598e80ff314bc9516ed4 NeedsCompilation: no Package: ChIPseeker Version: 1.0.11 Depends: R (>= 2.10) Imports: AnnotationDbi, BiocGenerics, IRanges, GenomicFeatures, GenomicRanges, ggplot2, gplots, grDevices, gtools, Matrix, plyr, RColorBrewer, rtracklayer, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: clusterProfiler, ReactomePA, DOSE, GOSemSim, org.Hs.eg.db, knitr License: Artistic-2.0 MD5sum: fd61b801f9edfede55ea57e480cd94a5 NeedsCompilation: no Package: chipseq Version: 1.14.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.4), GenomicRanges (>= 1.7.7), BSgenome, ShortRead Imports: methods, BiocGenerics, IRanges, BSgenome, GenomicRanges, lattice, ShortRead, stats Suggests: GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene License: Artistic-2.0 MD5sum: c0621ae77e3ffd63ab40526f2af6d316 NeedsCompilation: yes Package: ChIPseqR Version: 1.18.0 Depends: R (>= 2.10.0), methods, BiocGenerics, ShortRead Imports: Biostrings, fBasics, GenomicRanges, graphics, grDevices, HilbertVis, IRanges, methods, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: c25ce46ffe38e9f5bdd6ff21c78f5607 NeedsCompilation: yes Package: ChIPsim Version: 1.18.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: 9453a904ed1886d3647b18f65cde4c93 NeedsCompilation: no Package: ChIPXpress Version: 1.6.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 659868e1034bb843e834d89f5bee5f25 NeedsCompilation: no Package: chopsticks Version: 1.28.2 Depends: R(>= 2.10.0), survival, methods Suggests: hexbin License: GPL-3 MD5sum: bcd08f61dcc08cdbccfd7ef26a3d1a0a NeedsCompilation: yes Package: chroGPS Version: 1.8.1 Depends: R (>= 2.13.0), IRanges, methods, Biobase, MASS, graphics, stats, rgl, changepoint Imports: graphics, cluster, DPpackage, ICSNP Enhances: parallel, XML License: GPL (>= 2) MD5sum: 6524621d1d1d7b7fdc07a93b665a0cc8 NeedsCompilation: no Package: ChromHeatMap Version: 1.18.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: f939e0db9c117b7495a79c88692d5f4a NeedsCompilation: no Package: cisPath Version: 1.4.8 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) MD5sum: b54cb554f82bd671e98050b807e83799 NeedsCompilation: yes Package: cleanUpdTSeq Version: 1.2.0 Depends: R (>= 2.15), BiocGenerics (>= 0.1.0), BSgenome, BSgenome.Drerio.UCSC.danRer7, GenomicRanges, seqinr, e1071 License: GPL-2 MD5sum: 0ef73e6f65cff0fc0fbc24e1a2bebdbf NeedsCompilation: no Package: cleaver Version: 1.2.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), BRAIN, UniProt.ws (>= 2.1.4) License: GPL (>= 3) MD5sum: 7fc48c63811b9b48c6d094d9089cea2c NeedsCompilation: no Package: clippda Version: 1.14.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: 0626f3b9da6579ebef309bb37056ff52 NeedsCompilation: no Package: clipper Version: 1.4.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL Suggests: RUnit, BiocGenerics, RCytoscape (>= 1.6.3), graphite, ALL, hgu95av2.db, MASS, BiocStyle License: AGPL-3 MD5sum: f7dae06128a36ed7740f217aef2d7d43 NeedsCompilation: no Package: Clomial Version: 1.0.0 Depends: R (>= 2.10), matrixStats Imports: methods License: GPL (>= 2) MD5sum: 9546cf5bc99f19922eb123d6ba21c287 NeedsCompilation: no Package: Clonality Version: 1.12.0 Depends: R (>= 2.12.2), DNAcopy Imports: DNAcopy, grDevices, graphics, stats, utils Suggests: gdata, DNAcopy License: GPL-3 MD5sum: 870d2dd6dfd3df442c9675a59e352101 NeedsCompilation: no Package: clonotypeR Version: 1.2.1 Depends: methods Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan License: file LICENSE MD5sum: a83c79259582b494924e8f407274bb0b NeedsCompilation: no Package: clst Version: 1.12.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: 21485c9bcafbf2649d2b774cf01475eb NeedsCompilation: no Package: clstutils Version: 1.12.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit, RSVGTipsDevice License: GPL-3 MD5sum: c3443eb67f65a43504b6b43be3800dce NeedsCompilation: no Package: clusterProfiler Version: 1.12.0 Depends: R (>= 2.10), ggplot2 Imports: methods, stats4, plyr, AnnotationDbi, GO.db, KEGG.db, DOSE, GOSemSim Suggests: org.Hs.eg.db, ReactomePA, pathview, knitr License: Artistic-2.0 MD5sum: 45f083fa1a37f4455a323fa138e80cd2 NeedsCompilation: no Package: clusterStab Version: 1.36.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: 810ba2bc3d0f5b3e3d6df00eace367b2 NeedsCompilation: no Package: CMA Version: 1.22.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: 0d3bdb3c7e47cf038e746bbd489cda0c NeedsCompilation: no Package: CNAnorm Version: 1.10.1 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: 071e435ad7e216e9596421eef0307ebb NeedsCompilation: yes Package: CNEr Version: 1.0.0 Depends: R (>= 3.0.2) Imports: Biostrings(>= 2.26.3), RSQLite(>= 0.11.4), GenomicRanges(>= 1.12.5), rtracklayer(>= 1.20.4), XVector(>= 0.2.0), DBI(>= 0.2-7), GenomicAlignments(>= 0.99.17), methods, IRanges(>= 1.19.38) LinkingTo: IRanges, XVector Suggests: Gviz(>= 1.7.4), RUnit, BiocGenerics License: GPL-2 | file LICENSE License_restricts_use: yes MD5sum: 2f8f22531665f1a9103e83b508c69465 NeedsCompilation: yes Package: cn.farms Version: 1.12.0 Depends: R (>= 2.11), Biobase, methods, ff, oligoClasses, snow Imports: BiocGenerics, DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) MD5sum: ba5a0145956d63cb4d2f3377116e666d NeedsCompilation: yes Package: cn.mops Version: 1.10.1 Depends: R (>= 2.12), BiocGenerics, Biobase, IRanges, GenomicRanges Imports: methods, graphics, BiocGenerics, IRanges, Rsamtools, Suggests: snow, DNAcopy License: LGPL (>= 2.0) MD5sum: b1118ba1e0baa6e1c554e23ee95fd6d1 NeedsCompilation: yes Package: CNORdt Version: 1.6.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 7bbf10d5f254a2ba9eb24d9cae9ba8fe NeedsCompilation: yes Package: CNORfeeder Version: 1.4.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), graph Suggests: minet, catnet, igraph, Rgraphviz, RUnit, BiocGenerics License: GPL-3 MD5sum: 9a1fa2281aaf524e1e6068438e883fcc NeedsCompilation: no Package: CNORfuzzy Version: 1.6.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 5e77c1522b3a1655508b9fa3c38a387e NeedsCompilation: yes Package: CNORode Version: 1.6.0 Depends: CellNOptR (>= 1.5.14), genalg Enhances: MEIGOR License: GPL-2 MD5sum: ea36f32462502127ce5ac4e49cf694fa NeedsCompilation: yes Package: CNTools Version: 1.20.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: de1f6e1fb7122ad47c19bda5b6b2913c NeedsCompilation: yes Package: cnvGSA Version: 1.8.0 Depends: methods, brglm Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: 5d19d8affe06a36bfb831d6cab525154 NeedsCompilation: no Package: CNVrd2 Version: 1.2.0 Depends: R (>= 3.0.0), DNAcopy, methods, Rsamtools, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: IRanges Suggests: knitr License: GPL-2 MD5sum: 8db58ad7e656833b227f8cfe60dddd03 NeedsCompilation: no Package: CNVtools Version: 1.58.0 Depends: R (>= 2.10), survival License: GPL-3 MD5sum: 7f06763fad239e7291379b6c1875c356 NeedsCompilation: yes Package: cobindR Version: 1.2.0 Imports: yaml, seqinr, Biostrings, biomaRt, BSgenome, methods, gmp, mclust, rtfbs, gplots, IRanges Suggests: RUnit, BiocGenerics Enhances: rGADEM, seqLogo, genoPlotR, parallel, VennDiagram, RColorBrewer, vcd, MotifDb, snowfall License: Artistic-2.0 MD5sum: ec833ce7ffaef46859cf5f94741150fd NeedsCompilation: no Package: CoCiteStats Version: 1.36.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: a191811f328d438ebec08a09b8e095cf NeedsCompilation: no Package: codelink Version: 1.32.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: c792a2f178a192816ae6cad9aaea3dcb NeedsCompilation: no Package: CoGAPS Version: 1.14.0 Depends: R (>= 2.9.0), R.utils (>= 1.2.4), gplots (>= 2.8.0) Imports: graphics, grDevices, methods, stats, utils License: GPL (== 2) MD5sum: 8eb7975eef3d9aa12c7bfce1b611b040 NeedsCompilation: yes Package: coGPS Version: 1.8.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: fbd30267cd8019338e7de37fa975b0bf NeedsCompilation: no Package: COHCAP Version: 1.0.2 Depends: WriteXLS, COHCAPanno License: GPL-3 MD5sum: 6e13d6ded48057624875aa27e0e402d6 NeedsCompilation: no Package: COMPASS Version: 1.2.1 Depends: R (>= 3.0.2) Imports: Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.9.66), shiny, testthat, devtools, Kmisc License: Artistic-2.0 MD5sum: e2034a01ded660d06034bb3866d67fec NeedsCompilation: yes Package: compcodeR Version: 1.0.0 Depends: R (>= 3.0.2), sm Imports: tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, gdata, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods Suggests: BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>= 1.16.0), genefilter, NOISeq, DSS, TCC, samr, NBPSeq, HTSDiff Enhances: rpanel License: GPL (>= 2) MD5sum: b8d96859c1959e64a5a10cb75e9b5113 NeedsCompilation: no Package: CompGO Version: 1.0.0 Depends: RDAVIDWebService Imports: rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-2 MD5sum: 5eafaa817064c47cf84891f3d5cb854f NeedsCompilation: no Package: ConsensusClusterPlus Version: 1.18.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 4e59fa6dda93790133186b9e1e59acf8 NeedsCompilation: no Package: convert Version: 1.40.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: 36010f945f3369c8b3f8ed37ca4a415a NeedsCompilation: no Package: copa Version: 1.32.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 MD5sum: 094f7790a15d4f7e490fea4a2cafa0de NeedsCompilation: yes Package: COPDSexualDimorphism Version: 1.0.0 Depends: COPDSexualDimorphism.data, NCBI2R, RColorBrewer, beeswarm, limma, GenomicRanges, gplots, gtools License: LGPL-2.1 MD5sum: 138bddaaf2b419f2f1109b83ff609a57 NeedsCompilation: no Package: copynumber Version: 1.4.0 Depends: R (>= 2.10), BiocGenerics Imports: GenomicRanges, IRanges License: Artistic-2.0 MD5sum: bd1e5d41027d089486d40585960ee5ce NeedsCompilation: no Package: CopyNumber450k Version: 1.0.0 Depends: Biobase, minfi, DNAcopy, preprocessCore, BiocGenerics Imports: methods Suggests: CopyNumber450kData, minfiData License: Artistic-2.0 MD5sum: de5385faa8b9c1d714414d32ffa29264 NeedsCompilation: no Package: Cormotif Version: 1.10.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: 6d1f677a5aab1fc7b96909c22c09b692 NeedsCompilation: no Package: CorMut Version: 1.6.0 Depends: seqinr,igraph License: GPL-2 MD5sum: 96d5b1ce0dec651430654cd1afbbec6d NeedsCompilation: no Package: coRNAi Version: 1.14.0 Depends: R (>= 2.10), cellHTS2, limma, locfit Imports: MASS, gplots, lattice, grDevices, graphics, stats License: Artistic-2.0 MD5sum: 1723569d9b141b0c548fd44e6fa8a31e NeedsCompilation: no Package: CORREP Version: 1.30.0 Imports: e1071, stats Suggests: cluster, MASS License: GPL (>= 2) MD5sum: bc5cb6ad2518fffab3f517769d862f09 NeedsCompilation: no Package: CoverageView Version: 1.0.0 Depends: R (>= 2.10), methods,Rsamtools,rtracklayer Imports: IRanges,GenomicRanges,GenomicAlignments,parallel,tools License: Artistic-2.0 MD5sum: a3208775662b10fe4537966b2e66a977 NeedsCompilation: no Package: cqn Version: 1.10.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 MD5sum: 22e983fba5dc000877159f015c28df6d NeedsCompilation: no Package: CRImage Version: 1.12.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: 09afdb6d422812dd57f76bd0ce98d105 NeedsCompilation: no Package: CRISPRseek Version: 1.0.3 Depends: R (>= 3.0.1), BiocGenerics, Biostrings, BSgenome Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 9c0bc98bcefdb427fbade986eccf5847 NeedsCompilation: no Package: crlmm Version: 1.22.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats, RUnit License: Artistic-2.0 MD5sum: 5e89bfe918fdf1202cbd98c0df7bf42f NeedsCompilation: yes Package: CSAR Version: 1.16.0 Depends: R (>= 2.15.0), IRanges, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: aa922abd8c192b07a7659db657d37518 NeedsCompilation: yes Package: CSSP Version: 1.2.0 Imports: methods, splines, stats, utils Suggests: testthat License: GPL-2 MD5sum: 0bf70eade132209a9c4deefb894e1614 NeedsCompilation: yes Package: ctc Version: 1.38.0 Depends: amap License: GPL-2 MD5sum: 62ed7094dcd1f192af0efe7cad346846 NeedsCompilation: no Package: cummeRbund Version: 2.6.1 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics Suggests: cluster, plyr License: Artistic-2.0 MD5sum: f77ff3ff88e8859c7567f29c4e8d0245 NeedsCompilation: no Package: customProDB Version: 1.4.1 Depends: R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt Imports: IRanges, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.13.15), biomaRt (>= 2.17.1), stringr, RCurl, plyr, VariantAnnotation (>= 1.7.28), rtracklayer, RSQLite, AnnotationDbi Suggests: BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 2f29dac027b748d463166cf499ec31cd NeedsCompilation: no Package: cycle Version: 1.18.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: 6253dcb0a4634fe68682f424581c8014 NeedsCompilation: no Package: dagLogo Version: 1.2.1 Depends: R (>= 3.0.1), methods, biomaRt, grImport, grid, motifStack Imports: pheatmap, Biostrings Suggests: XML, UniProt.ws, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: 3fe6d10a6fd2e1601bf6b9b296e1d9c9 NeedsCompilation: no Package: daMA Version: 1.36.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 0e51eb88718f46f34a9ceca2e9030e8a NeedsCompilation: no Package: DART Version: 1.10.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 5e0014a26a94fbe356d1906353a4350d NeedsCompilation: no Package: DASiR Version: 1.4.0 Depends: IRanges, GenomicRanges, XML, Biostrings License: LGPL (>= 3) MD5sum: ddf13b17e58bf5727c6476f6aa6aad35 NeedsCompilation: no Package: DAVIDQuery Version: 1.24.0 Depends: RCurl (>= 1.4.0), utils License: GPL-2 MD5sum: cbfdcfcd28af1d2c2277ef2e6db00451 NeedsCompilation: no Package: DBChIP Version: 1.8.0 Depends: R (>= 2.15.0), edgeR, DESeq Suggests: ShortRead, BiocGenerics License: GPL (>= 2) MD5sum: cdd76a15a53abd6f83236fda520e3a19 NeedsCompilation: no Package: ddCt Version: 1.18.0 Depends: R (>= 2.3.0), Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, methods Suggests: RUnit License: LGPL-3 MD5sum: 7b847508a76969e56a4d30deac8362e9 NeedsCompilation: no Package: ddgraph Version: 1.8.0 Depends: graph, methods, Rcpp Imports: bnlearn (>= 2.8), gtools, pcalg, RColorBrewer, plotrix, MASS LinkingTo: Rcpp Suggests: Rgraphviz, e1071, ROCR, testthat License: GPL-3 MD5sum: 2e83ce65d13b26671116a2fba8b9bef5 NeedsCompilation: yes Package: DECIPHER Version: 1.10.1 Depends: R (>= 2.13.0), Biostrings (>= 2.31.9), RSQLite (>= 0.9), stats, parallel Imports: methods, IRanges, XVector LinkingTo: Biostrings, RSQLite, IRanges, XVector License: GPL-3 MD5sum: 00234637ffb9b006030a819093ffda6d NeedsCompilation: yes Package: DeconRNASeq Version: 1.6.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: 1553803ce31916da9b3008f7af82a5dd NeedsCompilation: no Package: DEDS Version: 1.38.0 Depends: R (>= 1.7.0) License: LGPL MD5sum: 749546bd1e79ce8f9e422f543460a2cc NeedsCompilation: yes Package: deepSNV Version: 1.10.0 Depends: R (>= 2.13.0), Rsamtools (>= 1.4.3), GenomicRanges, IRanges, Biostrings, VGAM, methods, graphics, VariantAnnotation (>= 1.5.0), parallel Imports: Rsamtools LinkingTo: Rsamtools Suggests: RColorBrewer, knitr License: GPL-3 MD5sum: 40c914044eca85d772860aa0f66a2978 NeedsCompilation: yes Package: DEGraph Version: 1.16.0 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 MD5sum: 522c10632986de9b8e71ffab8ade440d NeedsCompilation: no Package: DEGseq Version: 1.18.0 Depends: R (>= 2.8.0), qvalue, samr, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: b6c255d61076ecfd6bb8525ca4c3967b NeedsCompilation: yes Package: deltaGseg Version: 1.4.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: d20509303fb6c4c0d2462a725a8111ea NeedsCompilation: no Package: DESeq Version: 1.16.0 Depends: BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice Imports: genefilter, geneplotter, methods, MASS, RColorBrewer Suggests: pasilla (>= 0.2.10), vsn, gplots License: GPL (>= 3) MD5sum: 9ac328135956a365350cd8b2ab7841b6 NeedsCompilation: yes Package: DESeq2 Version: 1.4.5 Depends: GenomicRanges, IRanges, Rcpp (>= 0.10.1), RcppArmadillo (>= 0.3.4.4) Imports: BiocGenerics (>= 0.7.5), methods, locfit, genefilter, geneplotter, RColorBrewer, lattice LinkingTo: Rcpp, RcppArmadillo Suggests: RUnit, gplots, knitr, Biobase, BiocStyle, parathyroidSE, pasilla (>= 0.2.10), DESeq, vsn, GenomicAlignments, GenomicFeatures, Rsamtools, biomaRt License: GPL (>= 3) MD5sum: fa6375dbc3375a274d67d62353a347f6 NeedsCompilation: yes Package: DEXSeq Version: 1.10.8 Depends: Biobase, GenomicRanges, IRanges, DESeq2 (>= 1.3.69), BiocParallel Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter, RColorBrewer Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr Enhances: parallel License: GPL (>= 3) MD5sum: 9c34c44ab10e09a8785b98bf7278bfcc NeedsCompilation: no Package: dexus Version: 1.4.0 Depends: R (>= 2.15), methods, BiocGenerics Suggests: parallel, statmod, stats, DESeq, RColorBrewer License: LGPL (>= 2.0) MD5sum: 3f097edae0eb3615adfb1d0d44ea7b48 NeedsCompilation: yes Package: DFP Version: 1.22.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 MD5sum: 1a699db432a929b8646ce3807d3f7b12 NeedsCompilation: no Package: DiffBind Version: 1.10.2 Depends: R (>= 2.15.0), GenomicRanges, limma, GenomicAlignments Imports: RColorBrewer, amap, edgeR (>= 2.3.58), gplots, grDevices, stats, utils, IRanges, zlibbioc, lattice LinkingTo: Rsamtools Suggests: DESeq, Rsamtools, DESeq2, BiocStyle Enhances: rgl, parallel, BiocParallel License: Artistic-2.0 MD5sum: 2ad7cc3477cfef878f85af4a0d8722b7 NeedsCompilation: yes Package: diffGeneAnalysis Version: 1.46.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: ad214a89f49d20b0db5ab87190cfe510 NeedsCompilation: no Package: DirichletMultinomial Version: 1.6.0 Depends: IRanges Imports: stats4, methods Suggests: lattice, parallel, MASS, RColorBrewer, xtable License: LGPL-3 MD5sum: 02e348eb02f405a650995a56ea852b42 NeedsCompilation: yes Package: dks Version: 1.10.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: b0b862cf46432530ebd2e0a6c50f5791 NeedsCompilation: no Package: DMRcate Version: 1.0.2 Depends: R (>= 3.1.0), limma, minfi, DMRcatedata Imports: methods, graphics Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomicRanges License: file LICENSE MD5sum: 43f599acbd390c10b034e4a9301a55c4 NeedsCompilation: no Package: DMRforPairs Version: 1.0.2 Depends: R (>= 2.15.2), Gviz (>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges (>= 1.10.7), parallel License: GPL (>= 2) MD5sum: 84f410e2cb9323b22e43f780c4136fca NeedsCompilation: no Package: DNAcopy Version: 1.38.1 License: GPL (>= 2) MD5sum: 73d440a71c9a8229d7ecb3008fd4246a NeedsCompilation: yes Package: DNaseR Version: 1.2.0 Depends: R (>= 2.10.0), IRanges Imports: Rsamtools, GenomicRanges Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 7e01a561b2e067bd41d38e8c6dd8d51b NeedsCompilation: no Package: domainsignatures Version: 1.24.0 Depends: R (>= 2.4.0), KEGG.db, prada, biomaRt, methods Imports: AnnotationDbi License: Artistic-2.0 MD5sum: e642aad1174d8095b16c867f8bf4ce85 NeedsCompilation: no Package: DOSE Version: 2.2.1 Depends: R (>= 2.10), ggplot2 Imports: methods, plyr, qvalue, stats4, AnnotationDbi, DO.db, igraph, scales, reshape2, graphics, GOSemSim, grid Suggests: clusterProfiler, ReactomePA, knitr, org.Hs.eg.db License: Artistic-2.0 MD5sum: ca30538e9d35fd711bc9172e2632bc88 NeedsCompilation: no Package: DriverNet Version: 1.4.0 Depends: R (>= 2.10), methods License: GPL-3 MD5sum: e217dbd31ce32ed57ce44edc52df3513 NeedsCompilation: no Package: DrugVsDisease Version: 2.4.0 Depends: R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue Imports: annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, BiocGenerics, xtable License: GPL-3 MD5sum: 35804d826aef159fd0feaeacc2f5ea13 NeedsCompilation: no Package: DSS Version: 2.2.0 Depends: Biobase, locfdr Imports: methods,bsseq,edgeR License: GPL MD5sum: 669724a94da89344a15564af0c51ccbd NeedsCompilation: no Package: DTA Version: 2.10.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 MD5sum: fc8111bd719c3429282f51ebca6f7ba4 NeedsCompilation: no Package: dualKS Version: 1.24.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.0), affy, methods Imports: graphics License: LGPL (>= 2.0) MD5sum: 84ba6b368bb4801613ea1530718fd9e8 NeedsCompilation: no Package: dyebias Version: 1.22.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 MD5sum: 1f38929a71bd1f80f29b0261d6f576c4 NeedsCompilation: no Package: DynDoc Version: 1.42.0 Depends: methods, utils Imports: methods License: Artistic-2.0 MD5sum: 0225bb72c9c819a38cb55428a6a11862 NeedsCompilation: no Package: EasyqpcR Version: 1.7.0 Imports: plyr, matrixStats, plotrix, gWidgetsRGtk2 Suggests: SLqPCR, qpcrNorm, qpcR, knitr License: GPL (>= 2) MD5sum: 08f1c7321f98eb0231585b65fe2668f0 NeedsCompilation: no Package: easyRNASeq Version: 2.0.8 Imports: Biobase (>= 2.24.0), BiocGenerics (>= 0.10.0), biomaRt (>= 2.20.0), Biostrings (>= 2.32.1), DESeq (>= 1.16.0), edgeR (>= 3.6.6), genomeIntervals (>= 1.20.1), GenomicAlignments (>= 1.0.2), GenomicRanges (>= 1.16.3), graphics, IRanges (>= 1.22.9), LSD (>= 2.5), methods, parallel, Rsamtools (>= 1.16.1), ShortRead (>= 1.22.0), utils Suggests: BiocStyle (>= 1.2.0), BSgenome (>= 1.32.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.1000), GenomicFeatures (>= 1.16.2), RnaSeqTutorial (>= 0.2.0), RUnit (>= 0.4.26) License: Artistic-2.0 MD5sum: 16b42680ffff6b71b03960da00a88050 NeedsCompilation: no Package: EBarrays Version: 2.28.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) MD5sum: b8d963fd7d7fa417be25a8afdd690a44 NeedsCompilation: yes Package: EBcoexpress Version: 1.8.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) MD5sum: 810f603b6e9f07b0f88507f4e5288dd3 NeedsCompilation: yes Package: EBImage Version: 4.6.0 Imports: BiocGenerics (>= 0.7.1), methods, graphics, stats, abind, tiff, jpeg, png, locfit Suggests: BiocStyle License: LGPL MD5sum: 3852945c46db6144e64a0a5b1053a4fd NeedsCompilation: yes Package: EBSeq Version: 1.4.0 Depends: blockmodeling, gplots, R (>= 3.0.0) License: Artistic-2.0 MD5sum: 806b2b03d5e9b206994e74b98fe94731 NeedsCompilation: no Package: ecolitk Version: 1.36.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) MD5sum: 9b0af6c28edb5148b02a2c281fd25691 NeedsCompilation: no Package: EDASeq Version: 1.10.0 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 MD5sum: 1f368539ce5479a96126b2231a168a81 NeedsCompilation: no Package: EDDA Version: 1.0.2.1 Depends: Rcpp (>= 0.10.4),parallel,methods,ROCR,DESeq,baySeq,snow,edgeR Imports: graphics, stats, utils, parallel, methods, ROCR, DESeq, baySeq, snow, edgeR LinkingTo: Rcpp License: GPL (>= 2) MD5sum: 864dd2ea7bcda42c1d6e9c00fecc1b8e NeedsCompilation: yes Package: edgeR Version: 3.6.8 Depends: R (>= 2.15.0), limma Imports: methods Suggests: MASS, statmod, splines, locfit, KernSmooth License: GPL (>= 2) MD5sum: db37a933960facab951ae4b1d3e20893 NeedsCompilation: yes Package: eiR Version: 1.4.7 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods,ChemmineR,RCurl,digest, BiocGenerics LinkingTo: BH Suggests: RCurl,snow,BiocStyle,knitcitations,knitr License: Artistic-2.0 MD5sum: 70bdf9dc525f80c16e67b40f632de473 NeedsCompilation: yes Package: eisa Version: 1.16.0 Depends: isa2, Biobase (>= 2.17.8), AnnotationDbi, methods Imports: BiocGenerics, Category, genefilter, DBI Suggests: igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db License: GPL (>= 2) MD5sum: 606120eed4e94b1f83dbc3f40ef4a815 NeedsCompilation: no Package: ELBOW Version: 1.0.0 Depends: R (>= 2.15.0) Suggests: DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer License: file LICENSE License_is_FOSS: yes License_restricts_use: no MD5sum: 245b3018c3867e678b90d9bb02f389ff NeedsCompilation: no Package: ensemblVEP Version: 1.4.4 Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation Imports: Biostrings Suggests: RUnit License: Artistic-2.0 MD5sum: b807aac769cdfd2f1bdd9b8b8a9b7257 NeedsCompilation: no Package: ENVISIONQuery Version: 1.12.0 Depends: rJava, XML, utils License: GPL-2 MD5sum: 5ce01e155d1eaad0c9be2f5082743cef NeedsCompilation: no Package: epigenomix Version: 1.4.1 Depends: R (>= 2.12.0), methods, Biobase, IRanges, GenomicRanges Imports: BiocGenerics, beadarray License: LGPL-3 MD5sum: e22d34e68053f464f3936ab6902f46ee NeedsCompilation: no Package: epivizr Version: 1.2.12 Depends: R (>= 3.0.1), methods, Biobase, GenomicRanges (>= 1.13.47) Imports: httpuv (>= 1.3.0), rjson, IRanges Suggests: testthat, roxygen2, knitr, antiProfilesData, hgu133plus2.db, knitrBootstrap License: GPL-3 MD5sum: 0f50750faee51902f380b49b0eb0552f NeedsCompilation: no Package: ExiMiR Version: 2.6.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) License: GPL-2 MD5sum: 804025a8a480e2f49eed708faf2dddcf NeedsCompilation: no Package: exomeCopy Version: 1.10.0 Depends: IRanges, GenomicRanges, Rsamtools Imports: stats4, methods Suggests: Biostrings License: GPL (>= 2) MD5sum: 340ce1c371bb4550ce935f08c17d2ce3 NeedsCompilation: yes Package: exomePeak Version: 1.2.0 Depends: Rsamtools, GenomicFeatures (>= 1.0.0), rtracklayer License: GPL-2 MD5sum: c7858d1e75b57fb400eead5dcc54f078 NeedsCompilation: no Package: explorase Version: 1.28.1 Depends: R (>= 2.6.2) Imports: limma, rggobi, RGtk2 Suggests: cairoDevice License: GPL-2 MD5sum: c57898ef78259e0b3cf67b7163cc8793 NeedsCompilation: no Package: ExpressionView Version: 1.16.1 Depends: caTools, bitops, methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Imports: methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Suggests: ALL, hgu95av2.db, biclust, affy License: GPL (>= 2) MD5sum: c07a232f3f5fa4e982acd11a6d1a6a5a NeedsCompilation: yes Package: fabia Version: 2.10.2 Depends: R (>= 2.8.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 37a529382b6a2915fcbf5cb4682d0b62 NeedsCompilation: yes Package: factDesign Version: 1.40.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL MD5sum: 53a930237f3615e9164587b59aa42e43 NeedsCompilation: no Package: farms Version: 1.16.0 Depends: R (>= 2.8), affy (>= 1.20.0), MASS, methods Imports: affy, MASS, Biobase (>= 1.13.41), methods, graphics Suggests: affydata, Biobase, utils License: LGPL (>= 2.1) MD5sum: e25a7aaf40d30f1d6430032b50f32882 NeedsCompilation: no Package: fastLiquidAssociation Version: 1.0.0 Depends: methods, WGCNA, LiquidAssociation, parallel, stats Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 MD5sum: b100c685469f88f501249f415028ddbc NeedsCompilation: no Package: fastseg Version: 1.10.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: graphics, stats, IRanges, BiocGenerics Suggests: DNAcopy, oligo License: LGPL (>= 2.0) MD5sum: 86af608743e85bf3266b83209f60396c NeedsCompilation: yes Package: fdrame Version: 1.36.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: 7ddcc0f526f3a467339fb38531133f2c NeedsCompilation: yes Package: ffpe Version: 1.8.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: a47c95606ea9e9ac9d252b055d02de83 NeedsCompilation: no Package: FGNet Version: 2.0.0 Depends: R (>= 2.15) Imports: igraph (>= 0.6), RCurl, hwriter, R.utils, XML Suggests: RUnit, BiocGenerics, org.Sc.sgd.db Enhances: RColorBrewer, png, RDAVIDWebService License: GPL (>= 2) MD5sum: 81fca060d2a64ad6ac39431c268b5f8c NeedsCompilation: no Package: flagme Version: 1.20.1 Depends: gcspikelite, xcms Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) MD5sum: 02b340db9057b529b19008f262234dac NeedsCompilation: yes Package: flipflop Version: 1.2.2 Depends: R (>= 2.10.0) Imports: methods, Matrix, IRanges, GenomicRanges License: GPL-3 MD5sum: 19adfb7de09e3ae365ffc1af438d9891 NeedsCompilation: yes Package: flowBeads Version: 1.2.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: 5c389f898d080dac053a2b04daaa5189 NeedsCompilation: no Package: flowBin Version: 1.0.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 MD5sum: bccd86ab4ca6e02635681f05e2be54fe NeedsCompilation: no Package: flowCL Version: 1.0.0 Depends: R (>= 3.0.2), Rgraphviz, SPARQL Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 98e570d96ba2ef02fc29ffd05d5cd4fc NeedsCompilation: no Package: flowClust Version: 3.4.10 Depends: R(>= 2.5.0),methods, Biobase, graph, RBGL,ellipse, flowViz, mnormt, corpcor, flowCore, clue Imports: BiocGenerics, MCMCpack Suggests: parallel License: Artistic-2.0 MD5sum: 61dfeda48a8fd8be6e1892140ef258f9 NeedsCompilation: yes Package: flowCore Version: 1.30.7 Depends: R (>= 2.10.0) Imports: Biobase, BiocGenerics (>= 0.1.14), graph, graphics, methods, rrcov, stats, utils, stats4, corpcor Suggests: Rgraphviz, flowViz, ncdf, flowStats License: Artistic-2.0 MD5sum: 7177a569f428f3f807c741eea909ca4e NeedsCompilation: yes Package: flowCyBar Version: 1.0.0 Depends: R (>= 3.0.0) Imports: gplots, vegan, methods License: GPL-2 MD5sum: c55af5aeb19b6744141eba539a8df0ae NeedsCompilation: no Package: flowFit Version: 1.2.0 Depends: R (>= 2.12.2) Imports: flowCore, flowViz, graphics, methods, kza, minpack.lm, gplots Suggests: flowFitExampleData License: Artistic-2.0 MD5sum: d6c59b6bdc309f9776f2598570439264 NeedsCompilation: no Package: flowFlowJo Version: 1.22.0 Depends: R (>= 2.5.0), MASS, Imports: flowCore, XML (>= 1.96), methods, Biobase License: GPL (>= 3) MD5sum: f4f409dc0c9a57cf3cc0c3a863db2356 NeedsCompilation: no Package: flowFP Version: 1.22.0 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 MD5sum: f8860e08983e0b744ae616543ccb64bf NeedsCompilation: yes Package: flowMap Version: 1.99.2 Depends: R (>= 3.0.1), ade4(>= 1.5-2), doParallel(>= 1.0.3), abind(>= 1.4.0), reshape2(>= 1.2.2), ggplot2(>= 0.9.3.1), igraph (>= 0.7.1), scales(>= 0.2.3), Matrix(>= 1.1-4), gplots(>= 2.14.1), methods (>= 2.14) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 6441dc9e0cc33fb47d83efee209b0c12 NeedsCompilation: no Package: flowMatch Version: 1.1.2 Depends: R (>= 3.0.0), Rcpp (>= 0.11.0), methods, flowCore Imports: Biobase LinkingTo: Rcpp Suggests: healthyFlowData License: Artistic-2.0 MD5sum: 15bbfe672c7586f69887a3abcb5d0684 NeedsCompilation: yes Package: flowMeans Version: 1.16.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 MD5sum: 692c026eb94877285568c0e7523f9874 NeedsCompilation: no Package: flowMerge Version: 2.12.0 Depends: graph,feature,flowClust,Rgraphviz,foreach,snow Imports: rrcov,flowCore, graphics, methods, stats, utils Enhances: doMC, multicore License: Artistic-2.0 MD5sum: c13f2e2b79d1a920d64846fc4fdc2e59 NeedsCompilation: no Package: flowPeaks Version: 1.6.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 MD5sum: a34e6a5f5e2a725e15d507ffc03e0838 NeedsCompilation: yes Package: flowPhyto Version: 1.16.0 Depends: R (>= 1.8.0) Imports: flowClust, flowCore, flowMeans, TTR, caroline(>= 0.6.6) Suggests: RPostgreSQL, zoo, maps, mapdata, plotrix License: Artistic-2.0 MD5sum: 692bd992d261fa0c58da1b020e445bea NeedsCompilation: no Package: flowPlots Version: 1.12.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 MD5sum: afa29dc1241c5e8aa8a6a7ac3e6d511d NeedsCompilation: no Package: flowQ Version: 1.24.6 Depends: R (>= 2.10.0), methods, BiocGenerics, outliers, lattice, flowViz, mvoutlier, bioDist, parody, RColorBrewer, latticeExtra Imports: methods, BiocGenerics, geneplotter, flowCore, flowViz, IRanges Suggests: flowStats License: Artistic-2.0 MD5sum: 9b0653d2790105e53cabb04477272769 NeedsCompilation: no Package: flowQB Version: 1.6.0 Imports: Biobase, graphics,methods, flowCore,stats,MASS Suggests: MASS, flowCore, xtable License: Artistic-2.0 MD5sum: 62f09d555089fd032fac75d736a42149 NeedsCompilation: no Package: flowStats Version: 3.22.6 Depends: R (>= 2.10), flowCore, fda (>= 2.2.6), mvoutlier, cluster, flowWorkspace Imports: BiocGenerics, MASS, flowViz, flowCore, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, utils, KernSmooth, lattice,ks Suggests: xtable Enhances: RBGL,ncdfFlow,graph License: Artistic-2.0 MD5sum: 8f1476aadd064e990b6283ed6e5fe9bb NeedsCompilation: no Package: flowTrans Version: 1.16.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: 000181a607edeeb3c019c66b15807afe NeedsCompilation: no Package: flowType Version: 2.2.0 Depends: R (>= 2.10), Rcpp (>= 0.10.4), BH (>= 1.51.0-3) Imports: Biobase, graphics, grDevices, methods, flowCore, flowMeans, sfsmisc, rrcov, flowClust, flowMerge, stats LinkingTo: Rcpp, BH Suggests: xtable License: Artistic-2.0 MD5sum: 4307ad7805898c291cf672c608075c0e NeedsCompilation: yes Package: flowUtils Version: 1.28.0 Depends: R (>= 2.2.0), flowCore (>= 1.29.20) Imports: Biobase, graph, methods, stats, utils, flowViz, corpcor, RUnit, XML Suggests: gatingMLData License: Artistic-2.0 MD5sum: ed9a5b797b7dfd3a49c28b4ec8e8f44d NeedsCompilation: no Package: flowViz Version: 1.28.22 Depends: R (>= 2.7.0), flowCore, lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace, flowStats,knitr License: Artistic-2.0 MD5sum: d1226d404c7a852b2302ff080185ca70 NeedsCompilation: no Package: flowWorkspace Version: 3.10.09 Depends: R (>= 2.16.0),flowCore,flowViz,ncdfFlow,gridExtra Imports: Biobase, BiocGenerics, graph, graphics, lattice, methods, stats, stats4, utils, RBGL, graph, XML, Biobase, IDPmisc, Cairo, tools,hexbin,gridExtra,Rgraphviz ,data.table ,plyr ,latticeExtra ,Rcpp LinkingTo: Rcpp Suggests: testthat ,flowWorkspaceData ,RSVGTipsDevice License: Artistic-2.0 MD5sum: 6b9618c6e53b8a91f42fe1d65644d51b NeedsCompilation: yes Package: fmcsR Version: 1.6.5 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods,ChemmineR, BiocGenerics,parallel Suggests: BiocStyle,knitr,knitcitations License: Artistic-2.0 MD5sum: 19cf0d0890a1f6d2844a14271f0971f3 NeedsCompilation: yes Package: FRGEpistasis Version: 1.0.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: 29987d18050b725581ec5cd777e7f049 NeedsCompilation: no Package: frma Version: 1.16.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: e8d53f66c66cf5880b8766b9bd4118db NeedsCompilation: no Package: frmaTools Version: 1.16.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 5c206f9057405099448eebf06dccbbfc NeedsCompilation: no Package: FunciSNP Version: 1.6.0 Depends: R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data Imports: AnnotationDbi, IRanges, Rsamtools (>= 1.6.1), rtracklayer(>= 1.14.1), methods, ChIPpeakAnno (>= 2.2.0), GenomicRanges, VariantAnnotation, plyr, org.Hs.eg.db, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales Enhances: parallel License: GPL-3 MD5sum: 8240f7e41c6dec70b12dd458669e28bd NeedsCompilation: no Package: gaga Version: 2.10.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: dce145926cfc557fe6c34ccea4156392 NeedsCompilation: yes Package: gage Version: 2.14.4 Depends: R (>= 2.10) Imports: graph, KEGGREST, AnnotationDbi Suggests: pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 1e7bd8170afda306ea4c965e2dd57e8e NeedsCompilation: no Package: gaggle Version: 1.32.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) MD5sum: c36a31aff6b7dd162d7f9ed0c1cc0122 NeedsCompilation: no Package: gaia Version: 2.8.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 7e34603494fd8fd9a2e34f546dc6b827 NeedsCompilation: no Package: gaucho Version: 1.0.0 Depends: R (>= 3.0.0), compiler, GA, graph, heatmap.plus, png, Rgraphviz Suggests: knitr License: GPL-3 MD5sum: d5cfab3fda56d7c69d7bf181912de942 NeedsCompilation: no Package: gCMAP Version: 1.8.0 Depends: GSEABase, limma (>= 3.15.14) Imports: Biobase, BiocGenerics, methods, GSEAlm, Category, Matrix (>= 1.0.9), parallel, annotate, genefilter, AnnotationDbi Suggests: DESeq, KEGG.db, reactome.db, RUnit, GO.db, mgsa Enhances: bigmemory, bigmemoryExtras (>= 1.1.2) License: Artistic-2.0 MD5sum: 193423c8492aec438a72cb8789a41a60 NeedsCompilation: no Package: gCMAPWeb Version: 1.4.0 Depends: brew, gCMAP (>= 1.3.0), R (>= 2.15.0), yaml, Rook Imports: Biobase, annotate, AnnotationDbi, BiocGenerics, brew, graphics, grDevices, GSEABase, hwriter, IRanges, methods, parallel, stats, utils Suggests: org.Hs.eg.db, org.Mm.eg.db, ArrayExpress, affy, hgfocus.db, ArrayExpress, hgu133a.db, mgug4104a.db, RUnit Enhances: bigmemory, bigmemoryExtras License: Artistic-2.0 MD5sum: 99debdfbb245950b359d5f2eb97c93b0 NeedsCompilation: no Package: gcrma Version: 2.36.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocInstaller Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: 83670f84d95af4c514aef8453b6dab1b NeedsCompilation: yes Package: genArise Version: 1.40.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: a7e2621a4436d2fd49cd5cf416a2f319 NeedsCompilation: no Package: GeneAnswers Version: 2.6.2 Depends: R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer Imports: RBGL, annotate Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph License: LGPL (>= 2) MD5sum: 9b0365b530f516213a55aa8328fd644a NeedsCompilation: no Package: GENE.E Version: 1.4.1 Depends: R (>= 2.7.0), rhdf5 (>= 2.8.0), RCurl (>= 1.6-6) Imports: rhdf5, RCurl Suggests: RUnit, BiocGenerics, knitr, golubEsets (>= 1.0) License: GPL-2 MD5sum: 357db0a3581ba96013e925816410740d NeedsCompilation: no Package: GeneExpressionSignature Version: 1.10.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 MD5sum: 130206ff3f88fdf7a6e7ddf2ca274147 NeedsCompilation: no Package: genefilter Version: 1.46.1 Imports: AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10), graphics, methods, stats, survival Suggests: Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets, ALL, ROC, DESeq, pasilla License: Artistic-2.0 MD5sum: 4b4e0e82045422f1e80d6c99a8c8b5e7 NeedsCompilation: yes Package: genefu Version: 1.14.0 Depends: survcomp, mclust, biomaRt, R (>= 2.10) Imports: amap Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable License: Artistic-2.0 MD5sum: e186455b7272d8ba8f578593aee1df44 NeedsCompilation: no Package: GeneGA Version: 1.14.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 4d43dc790dc78a3ab331cdcdd0605ade NeedsCompilation: no Package: GeneMeta Version: 1.36.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: 48b9429650cc0cb88153b948b923cfa4 NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.6.1 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13), graph Imports: plyr, graph LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, Rgraphviz, XML, RCytoscape, RBGL License: GPL (>= 2) MD5sum: 01e2c297c36d6441f7179fda3f4b0c5b NeedsCompilation: yes Package: GeneOverlap Version: 1.0.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 5be2b6992a1489954915ba8558cd196b NeedsCompilation: no Package: geneplotter Version: 1.42.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 MD5sum: 456d94044f57a6dab466f0f922626f40 NeedsCompilation: no Package: geneRecommender Version: 1.36.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: be3752d69fb6160ef734b19a41ca94e1 NeedsCompilation: no Package: GeneRegionScan Version: 1.20.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: d144dd46f799dfcf662df7cf161cf096 NeedsCompilation: no Package: geneRxCluster Version: 1.0.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 2611cac0d33f09017dc124090764d407 NeedsCompilation: yes Package: GeneSelectMMD Version: 2.8.1 Depends: R (>= 2.13.2), Biobase Imports: Biobase, MASS, graphics, stats, survival, limma Suggests: ALL License: GPL (>= 2) MD5sum: 4e19c6317523f525d13dd24381cbce58 NeedsCompilation: yes Package: GeneSelector Version: 2.14.0 Depends: R (>= 2.5.1), methods, stats, Biobase Imports: multtest, siggenes, samr, limma Suggests: multtest, siggenes, samr, limma License: GPL (>= 2) MD5sum: c83faa8b3650faeafd238608ffb8fcaa NeedsCompilation: yes Package: geNetClassifier Version: 1.4.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, ipred, graphics Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph License: GPL (>= 2) MD5sum: bb0a3526e774ede08e18b25ff40fbacb NeedsCompilation: no Package: GeneticsDesign Version: 1.32.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 MD5sum: 2241ff6e21cd604c2345e800030507e9 NeedsCompilation: no Package: GeneticsPed Version: 1.26.0 Depends: R (>= 2.4.0), gdata (>= 2.3.0), genetics (>= 1.3.0), MASS Suggests: RUnit, gtools License: LGPL (>= 2.1) MD5sum: e3610c37688dd8eaff7af157ab538dfb NeedsCompilation: yes Package: genoCN Version: 1.16.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 66864ace2d9ae29005c65c81f0a4e3f6 NeedsCompilation: yes Package: GenomeGraphs Version: 1.24.0 Depends: R (>= 2.10), methods, biomaRt, grid License: Artistic-2.0 MD5sum: 283281a723234a09665b87b4ed6e2bc4 NeedsCompilation: no Package: GenomeInfoDb Version: 1.0.2 Depends: R (>= 3.1) Suggests: BiocGenerics, IRanges, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 82f4b1fefb6286ec3e31122dc561513c NeedsCompilation: no Package: genomeIntervals Version: 1.20.1 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.10.0) License: Artistic-2.0 MD5sum: 10a092f5d2df223cf5e8646ab36995ab NeedsCompilation: no Package: genomes Version: 2.10.0 Depends: R (>= 2.11), XML, RCurl, GenomicRanges, IRanges, Biostrings License: Artistic-2.0 MD5sum: a9f8dfbc2d98389eecbbc294bd595e9b NeedsCompilation: no Package: GenomicAlignments Version: 1.0.6 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.7.7), IRanges (>= 1.21.25), GenomicRanges (>= 1.15.32), Biostrings (>= 2.31.10), Rsamtools (>= 1.15.26), BSgenome (>= 1.31.12) Imports: methods, stats, BiocGenerics, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: IRanges Suggests: rtracklayer, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq, edgeR, RUnit, BiocStyle License: Artistic-2.0 MD5sum: a5c186ec5981de85b5bad15aa962f5f9 NeedsCompilation: yes Package: GenomicFeatures Version: 1.16.3 Depends: BiocGenerics (>= 0.1.0), IRanges (>= 1.17.13), GenomicRanges (>= 1.15.25), AnnotationDbi (>= 1.25.7) Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), Biostrings (>= 2.23.2), rtracklayer (>= 1.15.1), biomaRt (>= 2.17.1), RCurl, utils, Biobase (>= 2.15.1), GenomeInfoDb Suggests: org.Mm.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14), BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), Rsamtools, pasillaBamSubset (>= 0.0.5), seqnames.db, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: f9add92a7d35899508620c35daf3e504 NeedsCompilation: no Package: GenomicFiles Version: 1.0.1 Depends: R (>= 3.1.0), methods, BiocGenerics, BiocParallel, Rsamtools, rtracklayer (>= 1.23.16) Imports: GenomicAlignments Suggests: genefilter, deepSNV, BiocStyle, IRanges, RUnit, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 7ae084abebfb46a2edd5c771dffbe62d NeedsCompilation: no Package: GenomicRanges Version: 1.16.4 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.7.7), IRanges (>= 1.21.33), GenomeInfoDb (>= 0.99.17) Imports: methods, utils, stats, BiocGenerics, IRanges, XVector LinkingTo: IRanges, XVector (>= 0.3.4) Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, Biostrings (>= 2.25.3), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, KEGG.db, KEGGgraph, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Athaliana.BioMart.plantsmart21, seqnames.db, org.Sc.sgd.db, VariantAnnotation, edgeR, DESeq, DEXSeq, pasilla, pasillaBamSubset, RUnit, digest, BiocStyle License: Artistic-2.0 MD5sum: 406963a4a54c323940541356b74450ef NeedsCompilation: yes Package: Genominator Version: 1.18.0 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 MD5sum: 9d717ed9f6b46e7e29ed957d63574ca7 NeedsCompilation: no Package: genoset Version: 1.16.2 Depends: R (>= 2.10), BiocGenerics (>= 0.1.6), Biobase (>= 2.15.1), IRanges, GenomicRanges Imports: methods, graphics Suggests: RUnit, DNAcopy, stats, BSgenome, Biostrings Enhances: parallel License: Artistic-2.0 MD5sum: df576860d50b8c512853471781c0abfc NeedsCompilation: yes Package: GEOmetadb Version: 1.24.0 Depends: GEOquery,RSQLite License: Artistic-2.0 MD5sum: 043e3f31d9b88de1e4e60f3b7e0734af NeedsCompilation: no Package: GEOquery Version: 2.30.1 Depends: methods, Biobase Imports: XML, RCurl Suggests: limma License: GPL-2 MD5sum: d9404d31c641515160c3e0590398883a NeedsCompilation: no Package: GEOsubmission Version: 1.16.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: 320002da29dd9c80bd398d570880715d NeedsCompilation: no Package: GEWIST Version: 1.8.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: f75d0f0ec1ea617dd4b0f49a6ccef182 NeedsCompilation: no Package: GGBase Version: 3.26.1 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, Matrix, AnnotationDbi, digest Suggests: GGtools License: Artistic-2.0 MD5sum: 85aa827550f6d2f9b2abd024a6d4b64e NeedsCompilation: no Package: ggbio Version: 1.12.10 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, biovizBase(>= 1.12.1), reshape2, gtable, Biobase, IRanges (>= 1.21.19), GenomicRanges (>= 1.13.3), GenomicFeatures, Rsamtools (>= 1.13.1), GenomicAlignments, BSgenome, gridExtra, scales, VariantAnnotation, Hmisc, rtracklayer, Biostrings Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, Homo.sapiens License: Artistic-2.0 MD5sum: 822859e50351a2a27cb9f91c4c3cb3f6 NeedsCompilation: no Package: GGtools Version: 5.0.0 Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table Imports: methods, utils, stats, BiocGenerics, snpStats, ff, Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin, rtracklayer, Gviz, stats4, IRanges, GenomicRanges, iterators, Biostrings, ROCR, biglm Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP.20120608, multtest Enhances: MatrixEQTL, Homo.sapiens, foreach, doParallel, gwascat, ggplot2, reshape2 License: Artistic-2.0 MD5sum: 5e7b26427a318dd41907b397b78c0047 NeedsCompilation: no Package: girafe Version: 1.16.1 Depends: R (>= 2.10.0), methods, IRanges (>= 1.3.53), Rsamtools, ShortRead (>= 1.3.21), intervals (>= 0.13.1), genomeIntervals (>= 1.7.3), grid Imports: methods, Biobase, Biostrings, BSgenome, graphics, grDevices, stats, utils, IRanges Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 MD5sum: 1a31ca115449f4ef387a50024eaa62ae NeedsCompilation: yes Package: GLAD Version: 2.28.1 Depends: R (>= 2.10) Suggests: aws, tcltk License: GPL-2 MD5sum: 4ed5f84d5410180d31e7271b99ee3d1b NeedsCompilation: yes Package: GlobalAncova Version: 3.32.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi Suggests: Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db, vsn, GSEABase, Rgraphviz License: GPL (>= 2) MD5sum: 2f9389f2ac06e62c63d49ebb7415c625 NeedsCompilation: yes Package: globaltest Version: 5.18.0 Depends: methods Imports: Biobase, survival, AnnotationDbi, annotate, multtest, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, annotate, Biobase, survival, GSEABase, penalized, gss, MASS, boot, rpart License: GPL (>= 2) MD5sum: dd62bd3870c7b6d55dd34cb1f43799b5 NeedsCompilation: no Package: gmapR Version: 1.6.6 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools, Biobase, BSgenome, GenomicAlignments Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: fd842ac473ce7f9c5a0e53adfabbb39e NeedsCompilation: yes Package: GOFunction Version: 1.12.0 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) MD5sum: 0912922dd4c6b5da390e647d6064886f NeedsCompilation: no Package: goProfiles Version: 1.26.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db License: GPL-2 MD5sum: af2956f6e67610ade4266c229a3761af NeedsCompilation: no Package: GOSemSim Version: 1.22.0 Depends: R (>= 2.10), Rcpp Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db, Rcpp LinkingTo: Rcpp Suggests: DOSE, clusterProfiler, BiocInstaller, knitr License: GPL-2 MD5sum: 94b75cbf01b0b45d9fa948be0e860618 NeedsCompilation: yes Package: goseq Version: 1.16.2 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase Imports: mgcv, graphics, stats, utils, AnnotationDbi Suggests: GO.db, edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) MD5sum: 1261d940aa858bf85f2f6d6396b2759f NeedsCompilation: no Package: GOSim Version: 1.6.0 Depends: GO.db, annotate, igraph Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp, utils LinkingTo: Rcpp License: GPL (>= 2) MD5sum: 66ebbdab3720ea55f728c2f4524e44de NeedsCompilation: yes Package: GOstats Version: 2.30.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.3.26), graph Imports: AnnotationDbi (>= 0.0.89), Biobase (>= 1.15.29), Category (>= 2.3.26), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), graph (>= 1.15.15), methods, stats , AnnotationForge Suggests: hgu95av2.db (>= 1.13.0), ALL, GO.db (>= 1.13.0), annotate, multtest, genefilter, RColorBrewer, Rgraphviz, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 480bc0a7396da89f96f1fdb075d9a4a9 NeedsCompilation: no Package: GOTHiC Version: 1.1.2 Depends: R (>= 2.15.1), methods, utils, stats, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, IRanges, ShortRead, rtracklayer, ggplot2 Suggests: HiCDataLymphoblast Enhances: multicore License: GPL-3 MD5sum: 00dc19979d3349103e34de4a0574b1bb NeedsCompilation: no Package: goTools Version: 1.38.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: a9df02e28b77cc72b9553f98377a9777 NeedsCompilation: no Package: gpls Version: 1.36.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: e45729b3b77097d12ba3e7986dc75be5 NeedsCompilation: no Package: gprege Version: 1.8.0 Depends: R (>= 2.8.0), gptk Suggests: spam License: AGPL-3 MD5sum: 218c5f02c875d3bf90ad5a85108e92a5 NeedsCompilation: no Package: graph Version: 1.42.0 Depends: R (>= 2.10), methods Imports: methods, stats, stats4, tools, utils, BiocGenerics (>= 0.1.11) Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster Enhances: Rgraphviz License: Artistic-2.0 MD5sum: a16db6406a20f9cd94eea569a72c1a7c NeedsCompilation: yes Package: GraphAlignment Version: 1.28.0 License: file LICENSE License_restricts_use: yes MD5sum: 9c5aee815bee1d941f2c4252a8dec814 NeedsCompilation: yes Package: GraphAT Version: 1.36.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: 29f9a34dbd7828b3342d2cda4e3159e3 NeedsCompilation: no Package: graphite Version: 1.10.1 Depends: R (>= 2.10) Imports: AnnotationDbi, graph, graphics, methods, org.Hs.eg.db, stats, utils Suggests: BiocStyle, DEGraph (>= 1.4), hgu133plus2.db, RCytoscape (>= 1.6), SPIA (>= 2.2), topologyGSA (>= 1.4.0), clipper, ALL License: AGPL-3 MD5sum: 1f58e4c93e0aa82f76546ae687421462 NeedsCompilation: no Package: GraphPAC Version: 1.6.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 653c7ccfa60355df7a3a89b150888c3c NeedsCompilation: no Package: GRENITS Version: 1.16.1 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) MD5sum: 01a8a1e229227b76db41b5710e8b8500 NeedsCompilation: yes Package: GSCA Version: 1.2.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5 Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: 60c2e9a0025c6e3f57ef8fe6e6bbb3fd NeedsCompilation: no Package: GSEABase Version: 1.26.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), annotate, methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools License: Artistic-2.0 MD5sum: 4ee5caef78742e62fca5c354bd8546b3 NeedsCompilation: no Package: GSEAlm Version: 1.24.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 77efcbe571e563199ba6ba692b4ac91d NeedsCompilation: no Package: GSRI Version: 2.12.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: 06e42fd267710d5f596b976df8b967a7 NeedsCompilation: no Package: GSVA Version: 1.12.0 Depends: R (>= 2.13.0), methods, GSEABase (>= 1.17.4) Imports: methods, BiocGenerics, Biobase, GSEABase Suggests: limma, RColorBrewer, genefilter, mclust, edgeR, GSVAdata Enhances: snow, parallel License: GPL (>= 2) MD5sum: 5411ddaa92885bc8fd8998ae6afc298f NeedsCompilation: yes Package: Gviz Version: 1.8.4 Depends: R (>= 2.10.0), methods, grid, BiocGenerics (>= 0.1.4) Imports: IRanges (>= 1.19.5), XVector, rtracklayer (>= 1.15.5), lattice, RColorBrewer, biomaRt (>= 2.11.0), GenomicRanges (>= 1.7.14), AnnotationDbi (>= 1.17.11), Biobase (>= 2.15.3), GenomicFeatures (>= 1.9.7), BSgenome (>= 1.31.5), Biostrings (>= 2.31.8), biovizBase (>= 1.5.7), Rsamtools(>= 1.11.1), latticeExtra(>= 0.6-26), matrixStats(>= 0.8.14), GenomicAlignments (>= 0.99.11) Suggests: xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle License: Artistic-2.0 MD5sum: a2dc8d12c4c59037fc4c35da1d5ba646 NeedsCompilation: no Package: gwascat Version: 1.8.0 Depends: R (>= 3.0.0) Imports: methods, Biostrings, IRanges, GenomicRanges, BiocGenerics, snpStats, Rsamtools, rtracklayer Suggests: DO.db, Gviz, ggbio, graph Enhances: SNPlocs.Hsapiens.dbSNP.20120608, pd.genomewidesnp.6 License: Artistic-2.0 MD5sum: 1d3389747866c206f4840b8c4b826a7e NeedsCompilation: no Package: GWASTools Version: 1.10.1 Depends: Biobase, ncdf, gdsfmt, sandwich Imports: methods, DBI, RSQLite, GWASExactHW, DNAcopy, survival, lmtest, quantsmooth Suggests: GWASdata, BiocGenerics, RUnit, SNPRelate, snpStats, VariantAnnotation License: Artistic-2.0 MD5sum: 3eac5093c3f3588a17bff922c2fa3a70 NeedsCompilation: no Package: h5vc Version: 1.4.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, IRanges, Biostrings, Rsamtools, methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, bit64 License: GPL (>= 3) MD5sum: 47551b03964675a00ca2e3fb6b1d8ff5 NeedsCompilation: yes Package: hapFabia Version: 1.6.3 Depends: R (>= 2.12.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 82ad7b8a62940f4f13832b28c764978c NeedsCompilation: yes Package: Harshlight Version: 1.36.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: dcbe712d97085b282c111bebc4081849 NeedsCompilation: yes Package: HCsnip Version: 1.4.0 Depends: R(>= 2.10.0), survival, coin, fpc, clusterRepro, impute, randomForestSRC, sm, sigaR, Biobase License: GPL (>= 2) MD5sum: 290cef0337839003daab1b0209a879b5 NeedsCompilation: no Package: Heatplus Version: 2.10.0 Imports: graphics, grDevices, stats Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: 46b59c9d9d10dfad2a68b696788b17b3 NeedsCompilation: no Package: HELP Version: 1.22.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) MD5sum: 713042c42987bbba9ff7a15dc3b6ecd5 NeedsCompilation: no Package: HEM Version: 1.36.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) MD5sum: f95c6bb89821631983f98a9e3abc3a5d NeedsCompilation: yes Package: HilbertVis Version: 1.22.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) MD5sum: 930b2160c8c5b213483b9770faae3ee7 NeedsCompilation: yes Package: HilbertVisGUI Version: 1.22.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) MD5sum: 8b43a3a006a88b6a2ae444909514d2fc NeedsCompilation: yes Package: HiTC Version: 1.8.1 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix Suggests: BiocStyle License: Artistic-2.0 MD5sum: 127d0020f9a3bb2c58293e336606725a NeedsCompilation: no Package: HMMcopy Version: 1.6.0 Depends: R (>= 2.10.0), IRanges (>= 1.4.16), geneplotter (>= 1.24.0) License: GPL-3 MD5sum: f6a75ae0846586362bf5f51bc76ef621 NeedsCompilation: yes Package: hopach Version: 2.24.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: Biobase, cluster, graphics, grDevices, methods, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: 916a20f958cfe15570fd61dbedd759fa NeedsCompilation: yes Package: hpar Version: 1.6.0 Depends: R (>= 2.15) Suggests: org.Hs.eg.db, GO.db, knitr License: Artistic-2.0 MD5sum: 832f8c9215b0395ed0817e700a807ecf NeedsCompilation: no Package: HTqPCR Version: 1.18.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 MD5sum: b1c0a54fda09622f1eb633ec8a9e3529 NeedsCompilation: no Package: HTSanalyzeR Version: 2.16.0 Depends: R (>= 2.15), igraph, methods Imports: graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt, RankProd Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow License: Artistic-2.0 MD5sum: 436e6c0895ace7f6212dd9a683bf3134 NeedsCompilation: no Package: HTSeqGenie Version: 3.14.1 Depends: R (>= 3.0.0), gmapR (>= 1.4.3), ShortRead (>= 1.19.13), VariantAnnotation (>= 1.8.3) Imports: BiocGenerics (>= 0.2.0), IRanges (>= 1.14.3), GenomicRanges (>= 1.7.12), Rsamtools (>= 1.8.5), Biostrings (>= 2.24.1), chipseq (>= 1.6.1), hwriter (>= 1.3.0), Cairo (>= 1.5.5), GenomicFeatures (>= 1.9.31), BiocParallel, parallel, tools, rtracklayer (>= 1.17.19), GenomicAlignments, VariantTools (>= 1.3.6) Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db License: Artistic-2.0 MD5sum: df2a6c81897aa374b8a26b038a826b61 NeedsCompilation: no Package: htSeqTools Version: 1.10.0 Depends: R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase, IRanges, methods, MASS, BSgenome, GenomicRanges Enhances: multicore License: GPL (>= 2) MD5sum: d81e600c07566dd6ba1c58dfe3289f38 NeedsCompilation: no Package: HTSFilter Version: 1.4.0 Depends: methods, Biobase (>= 2.16.0), R (>= 2.10.0) Imports: DESeq (>= 1.8.3), edgeR (>= 2.6.12), DESeq2 (>= 1.2.8), GenomicRanges, IRanges Suggests: EDASeq (>= 1.2.0) License: Artistic-2.0 MD5sum: 741d282dfada49f4b4299eef2476df83 NeedsCompilation: no Package: HybridMTest Version: 1.8.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) MD5sum: d93e52720cecdca5faea59f0829dacf0 NeedsCompilation: no Package: hyperdraw Version: 1.16.0 Depends: R (>= 2.9.0) Imports: methods, grid, graph, hypergraph, Rgraphviz, stats4 License: GPL (>= 2) MD5sum: f0d4c7965dcd550d3611b4cd1773426b NeedsCompilation: no Package: hypergraph Version: 1.36.0 Depends: R (>= 2.1.0), methods, graph License: Artistic-2.0 MD5sum: 3193faef5947d88e72e5b937115d7341 NeedsCompilation: no Package: iASeq Version: 1.8.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 MD5sum: 2a483a2cc78e1381643dc9f9e6858313 NeedsCompilation: no Package: iBBiG Version: 1.8.0 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 MD5sum: 9ada8b655d1e3f6ef8b6c840daf6f769 NeedsCompilation: yes Package: ibh Version: 1.12.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) MD5sum: a1fbf0c8e413a33f1457156d8583dcd6 NeedsCompilation: no Package: iBMQ Version: 1.4.2 Depends: R(>= 2.15.0),Biobase (>= 2.16.0), ggplot2 (>= 0.9.2) License: Artistic-2.0 MD5sum: fe43a0d0ec3fbda25f95c8d1bad9f45e NeedsCompilation: yes Package: Icens Version: 1.36.0 Depends: survival Imports: graphics License: Artistic-2.0 MD5sum: b574dcc37720c95eb3f42828ac99341d NeedsCompilation: no Package: iChip Version: 1.18.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: 9477b318d280f38c06065fc3e5b28c2c NeedsCompilation: yes Package: iClusterPlus Version: 1.0.1 Depends: R (>= 2.15.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 713fd272db475fd1474c5fab8fd15d9e NeedsCompilation: yes Package: idiogram Version: 1.40.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: 458f84df5922239911972b30c1147e39 NeedsCompilation: no Package: IdMappingAnalysis Version: 1.8.0 Depends: R (>= 2.14), R.oo (>= 1.13.0), rChoiceDialogs Imports: boot, mclust, RColorBrewer, Biobase License: GPL-2 MD5sum: c43fbb17173a1318b04c4a393e9a61a8 NeedsCompilation: no Package: IdMappingRetrieval Version: 1.10.0 Depends: R.oo, XML, RCurl, rChoiceDialogs, ENVISIONQuery Imports: biomaRt, ENVISIONQuery, DAVIDQuery, AffyCompatible, R.methodsS3, R.oo, utils License: GPL-2 MD5sum: 156601ae49ff2ed4cadae1186e487918 NeedsCompilation: no Package: illuminaio Version: 0.6.1 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: 5437f862010d901741ba69a52223211e NeedsCompilation: yes Package: imageHTS Version: 1.14.1 Depends: R (>= 2.9.0), EBImage (>= 4.3.12), cellHTS2 (>= 2.10.0) Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071 Suggests: BiocStyle, MASS License: LGPL-2.1 MD5sum: fcff26218b67ba6c4bcff6fde2a353e7 NeedsCompilation: no Package: impute Version: 1.38.1 Depends: R (>= 2.10) License: GPL-2 MD5sum: 5823554f46968e740beb24decb2e8587 NeedsCompilation: yes Package: INPower Version: 1.0.0 Depends: R (>= 3.1.0), mvtnorm Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 4801468a894aebf30118287842f450f8 NeedsCompilation: no Package: inSilicoDb Version: 2.0.1 Depends: R (>= 3.0.0), rjson, Biobase, RCurl Suggests: limma License: GPL-2 MD5sum: ddb9bbb963b91d0dd4e960664914cdc1 NeedsCompilation: no Package: inSilicoMerging Version: 1.8.7 Depends: R (>= 2.11.1), Biobase, DWD Suggests: BiocGenerics, inSilicoDb License: GPL-2 MD5sum: 1cba2018f08810a7bbdc0ab4dbdb633f NeedsCompilation: no Package: intansv Version: 1.4.1 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: Artistic-2.0 MD5sum: 81118315e3e4195992f0af746cf1820f NeedsCompilation: no Package: interactiveDisplay Version: 1.2.0 Depends: R (>= 2.10), methods, BiocGenerics, grid Imports: shiny, RColorBrewer, ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi Suggests: RUnit, hgu95av2.db, knitr,GenomicRanges, GOstats, ggbio, GO.db, Gviz, rtracklayer License: Artistic-2.0 MD5sum: d453619c0e52637dbf7feee88bacf619 NeedsCompilation: no Package: inveRsion Version: 1.12.1 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) MD5sum: 7f0c130d4cce9226b47edc74fb77adb8 NeedsCompilation: yes Package: iontree Version: 1.10.0 Depends: methods, rJava, RSQLite, XML Suggests: iontreeData License: GPL-2 MD5sum: 0278c1fe8ed5a975b404727fde28c896 NeedsCompilation: no Package: iPAC Version: 1.8.0 Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest License: GPL-2 MD5sum: 9bd24ebdc48f682d1e5694de5d5cf306 NeedsCompilation: no Package: IPPD Version: 1.12.0 Depends: R (>= 2.12.0), MASS, Matrix, XML, digest, bitops Imports: methods, stats, graphics License: GPL (>= 2) MD5sum: 9356472c325191fa1fcc856ca15930dd NeedsCompilation: yes Package: IRanges Version: 1.22.10 Depends: R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.9.1) Imports: methods, utils, stats, BiocGenerics, stats4 Suggests: XVector, GenomicRanges, BSgenome.Celegans.UCSC.ce2, RUnit License: Artistic-2.0 MD5sum: a59804d89234a109f4c33c08ffdc0acd NeedsCompilation: yes Package: iSeq Version: 1.16.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: a240d86badeab21e2549b329944c1ce5 NeedsCompilation: yes Package: isobar Version: 1.10.0 Depends: R (>= 2.10.0), Biobase, stats, methods, plyr Imports: distr Suggests: MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, distr, Rgbp, DBI, MASS License: LGPL-2 MD5sum: a6510ad27bef64100affc645c9d0211f NeedsCompilation: no Package: IsoGeneGUI Version: 1.20.0 Depends: tcltk, tkrplot, IsoGene Imports: multtest, relimp, WriteXLS,gdata, RColorBrewer, geneplotter Suggests: RUnit License: GPL-2 MD5sum: b8f2fc990a881b935ac862e7701ac6d2 NeedsCompilation: no Package: ITALICS Version: 2.24.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 MD5sum: 805ad4f9e4e09b4cd753d54e9823c4da NeedsCompilation: no Package: iterativeBMA Version: 1.22.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 762d124af7f331de01b22d5ef35974d6 NeedsCompilation: no Package: iterativeBMAsurv Version: 1.22.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) MD5sum: 8a71df1a3daae7fbe5fbbf67b2132fe4 NeedsCompilation: no Package: jmosaics Version: 1.4.0 Depends: R (>= 2.15.2), mosaics License: GPL (>= 2) MD5sum: 705fd59ddea55750045b9507fc6099dc NeedsCompilation: no Package: joda Version: 1.12.0 Depends: R (>= 2.0), bgmm, RBGL License: GPL (>= 2) MD5sum: 96902c2de63a8067decb319f040286e8 NeedsCompilation: no Package: KCsmart Version: 2.22.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 MD5sum: e8bfaabb7e803aca4ed681d2cdd01e3e NeedsCompilation: no Package: KEGGgraph Version: 1.22.1 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) MD5sum: 3ae43174602b2c6ff53bad4c2ff8944e NeedsCompilation: no Package: keggorthology Version: 2.16.1 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: 5a4c7e263f69bb8b9d461212218c4120 NeedsCompilation: no Package: KEGGprofile Version: 1.7.6 Imports: AnnotationDbi,png,TeachingDemos,XML,KEGG.db,KEGGREST,biomaRt License: GPL (>= 2) MD5sum: 5381c008f25b6e6f1c3e9d2aa5d49ab4 NeedsCompilation: no Package: KEGGREST Version: 1.4.1 Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, knitr License: Artistic-2.0 MD5sum: 86e45f7234415af3131128c9c7ea5582 NeedsCompilation: no Package: lapmix Version: 1.30.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) MD5sum: 21f0b14260af432eadc381fe4ee3e36c NeedsCompilation: no Package: LBE Version: 1.32.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue License: GPL-2 MD5sum: d2f392ba29b13368bbe108f998437690 NeedsCompilation: no Package: les Version: 1.14.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: d86978958ed5423699571031422257e7 NeedsCompilation: no Package: limma Version: 3.20.9 Depends: R (>= 2.3.0), methods Suggests: statmod (>= 1.2.2), splines, locfit, MASS, ellipse, affy, vsn, AnnotationDbi, org.Hs.eg.db, illuminaio License: GPL (>= 2) MD5sum: 6b7f93883b539ee041188c817240263b NeedsCompilation: yes Package: limmaGUI Version: 1.40.0 Depends: limma, tcltk Suggests: statmod, R2HTML, xtable, tkrplot License: LGPL MD5sum: c988af0820a62c28135ab052051c9ce9 NeedsCompilation: no Package: LiquidAssociation Version: 1.18.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: 6deba0c66419cb071134ef9a3e0fc364 NeedsCompilation: no Package: lmdme Version: 1.6.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) MD5sum: 11bbbcd2dfc119cffb007ff16b6fafc5 NeedsCompilation: no Package: LMGene Version: 2.20.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy Suggests: affydata License: LGPL MD5sum: 9bc838b16a81397220117e9bd030d5a3 NeedsCompilation: no Package: logicFS Version: 1.34.0 Depends: LogicReg, mcbiopi Suggests: genefilter, siggenes License: LGPL (>= 2) MD5sum: d9062dd896a1a464bbf24fd82b59b6ed NeedsCompilation: no Package: logitT Version: 1.22.0 Depends: affy Suggests: SpikeInSubset License: GPL (>= 2) MD5sum: 78440a8e4b608e6c96f0acf18e59d1a1 NeedsCompilation: yes Package: lol Version: 1.12.0 Depends: penalized, Matrix Imports: Matrix, penalized, graphics, grDevices, stats License: GPL-2 MD5sum: d2a173d3061d3f230b944f3a5e286b42 NeedsCompilation: no Package: LPE Version: 1.38.0 Depends: R (>= 2.10) Imports: stats License: LGPL MD5sum: 0fb8d874cce73d50bda12ad282314795 NeedsCompilation: no Package: LPEadj Version: 1.24.0 Depends: LPE Imports: LPE, stats License: LGPL MD5sum: f5a95f72e36f9cf58332fa1efd5c53c5 NeedsCompilation: no Package: lpNet Version: 1.4.0 Depends: lpSolve, nem License: Artistic License 2.0 MD5sum: d56d42d1269a4b555209601be6021a89 NeedsCompilation: no Package: lumi Version: 2.16.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, Biobase (>= 2.5.5), lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: 2fb8f9f3e57fc7f6fdb2c0cc4c83ac27 NeedsCompilation: no Package: LVSmiRNA Version: 1.14.3 Depends: R (>= 3.1.0), methods, splines Imports: BiocGenerics, stats4, graphics, stats, utils, MASS, Biobase, quantreg, limma, affy, SparseM, vsn Enhances: parallel,snow, Rmpi License: GPL-2 MD5sum: f999ca6912a066445e32ea99b8378b72 NeedsCompilation: yes Package: maanova Version: 1.34.1 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, stats, utils Suggests: qvalue, snow Enhances: Rmpi License: GPL (>= 2) MD5sum: e0b3df8908f9b1f5e8888d5a3be5b7db NeedsCompilation: yes Package: macat Version: 1.38.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem License: Artistic-2.0 MD5sum: 20f845aa5e245b8ae4eb417da5b5820d NeedsCompilation: no Package: maCorrPlot Version: 1.34.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) MD5sum: 9a91023e4f094d55ebe0ec0da9c25725 NeedsCompilation: no Package: made4 Version: 1.38.0 Depends: ade4, RColorBrewer,gplots,scatterplot3d Suggests: affy License: Artistic-2.0 MD5sum: 9cf02854697053ea74d3c84f57837915 NeedsCompilation: no Package: maigesPack Version: 1.28.1 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) MD5sum: 1ccce21dd467645f2baa53cffcf2c2be NeedsCompilation: yes Package: makecdfenv Version: 1.40.0 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) MD5sum: efdbbe43a0e1b08509d5a2fdd5635995 NeedsCompilation: yes Package: MANOR Version: 1.36.0 Depends: R (>= 2.10), GLAD Imports: GLAD, graphics, grDevices, stats, utils License: GPL-2 MD5sum: 4d9b26684ca1ea261ee39b3aa7947490 NeedsCompilation: yes Package: manta Version: 1.10.0 Depends: R (>= 1.8.0), methods, edgeR (>= 2.5.13) Imports: Hmisc, caroline(>= 0.6.6) Suggests: RSQLite, plotrix License: Artistic-2.0 MD5sum: f67a2cac277c414d0ab939bdde989e69 NeedsCompilation: no Package: MantelCorr Version: 1.34.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) MD5sum: 58bc162dfa7e52f09b2022c6507b461e NeedsCompilation: no Package: maPredictDSC Version: 1.2.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 MD5sum: 0b1cf1fcbad9efc927a3fabef0113cd9 NeedsCompilation: no Package: marray Version: 1.42.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL MD5sum: e46e9892bf435f9a6ec69386b35488ce NeedsCompilation: no Package: maSigPro Version: 1.36.0 Depends: R (>= 2.3.1), stats, Biobase, MASS Imports: Biobase, graphics, grDevices, limma, Mfuzz, stats, utils, MASS License: GPL (>= 2) MD5sum: 009fb7f19886ead93d8c9c7174c74c50 NeedsCompilation: no Package: maskBAD Version: 1.8.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe License: GPL (>= 2) MD5sum: ccc0fd73530ea4b8413cc57128792287 NeedsCompilation: no Package: MassArray Version: 1.16.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, methods, stats, utils License: GPL (>= 2) MD5sum: bfce9fc5ec879d4f1d0976e27c675c2d NeedsCompilation: no Package: massiR Version: 1.0.1 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2), Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: f179488138a1d84f7b7abc762de066f7 NeedsCompilation: no Package: MassSpecWavelet Version: 1.30.0 Depends: waveslim Suggests: xcms, caTools License: LGPL (>= 2) MD5sum: 314fab3a7206dfa4bad7b9f6fd66c3ee NeedsCompilation: yes Package: matchBox Version: 1.6.0 Depends: R (>= 2.8.0) License: Artistic-2.0 MD5sum: 00d5dee27e9bd52d28418ad24c0c378d NeedsCompilation: no Package: MBCB Version: 1.18.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) MD5sum: f8729f97f98a66a458a5c873c4e502ec NeedsCompilation: no Package: mBPCR Version: 1.18.0 Depends: oligoClasses, SNPchip Imports: Biobase Suggests: xtable License: GPL (>= 2) MD5sum: 8a7aad38f79834a3a116646e648c7fc5 NeedsCompilation: no Package: mcaGUI Version: 1.12.0 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) MD5sum: d831b0494086404d5bb9d539141a58a1 NeedsCompilation: no Package: MCRestimate Version: 2.20.0 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) MD5sum: 16d5289bb08d8e4e90cc1e7a5b3c2b48 NeedsCompilation: no Package: mdqc Version: 1.26.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) MD5sum: 719b496c9f4e5d3620fe4efa4f806be4 NeedsCompilation: no Package: MeasurementError.cor Version: 1.36.0 License: LGPL MD5sum: 99163185e87e12bdecd3e044dc4ff6be NeedsCompilation: no Package: MEDIPS Version: 1.14.0 Depends: R (>= 3.0), BSgenome, DNAcopy Imports: Biostrings, BSgenome, Rsamtools, graphics, gtools, IRanges, methods, stats, utils, GenomicRanges, edgeR, GenomicFeatures, DNAcopy, biomaRt, rtracklayer Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg19, MEDIPSData License: GPL (>= 2) MD5sum: d56ee712237548dd6c5afd9a86b1a809 NeedsCompilation: no Package: MEDME Version: 1.24.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) MD5sum: be9b14dbb954db167686d5c219e3738b NeedsCompilation: yes Package: MergeMaid Version: 2.36.0 Depends: R (>= 2.10.0), survival, Biobase, MASS, methods License: GPL (>= 2) MD5sum: 2e3b53141b3b32c8b1066d447da39300 NeedsCompilation: no Package: MeSHDbi Version: 1.0.2 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.16.10), DBI, RSQLite, IRanges, Biobase Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 15a3571f662126d25465ea7166f640ec NeedsCompilation: no Package: meshr Version: 1.0.4 Depends: R (>= 3.0.1), fdrtool, Category, BiocGenerics, methods, cummeRbund, org.Hs.eg.db, MeSH.db, MeSH.AOR.db, MeSH.PCR.db, MeSHDbi, org.MeSH.Hsa.db, org.MeSH.Aca.db, org.MeSH.Atu.K84.db, org.MeSH.Bsu.168.db, org.MeSH.Syn.db License: Artistic-2.0 MD5sum: 8bb3b43a030ac8d5ada57bf799bb8d11 NeedsCompilation: no Package: messina Version: 1.0.0 Depends: R (>= 3.1.0), survival (>= 2.37-4), methods Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) MD5sum: d174f8ec26599c6f307a911c1469d7d1 NeedsCompilation: yes Package: metaArray Version: 1.42.0 Imports: Biobase, MergeMaid, graphics, stats License: LGPL-2 MD5sum: fa4b1cbfd82c8193accd927ed4f8474f NeedsCompilation: yes Package: metagenomeSeq Version: 1.6.0 Depends: R(>= 3.0), Biobase, limma, matrixStats, methods, RColorBrewer, gplots Suggests: annotate, biom, parallel, vegan, knitr License: Artistic-2.0 MD5sum: 97d1238aff2f91fc9e626d8d84318d1c NeedsCompilation: no Package: metahdep Version: 1.22.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: bcc7b0e624c1ab42af949aeb8d2fd1e5 NeedsCompilation: yes Package: metaMS Version: 1.0.0 Depends: R (>= 2.10), methods, CAMERA, xcms (>= 1.35) Imports: Matrix, tools, robustbase, BiocGenerics Suggests: metaMSdata, RUnit License: GPL (>= 2) MD5sum: 4a44d10f494ef4da468c180a7c02b77a NeedsCompilation: no Package: metaSeq Version: 1.4.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: e5641c438048503486ca7e499ae50a0c NeedsCompilation: no Package: metaseqR Version: 1.2.3 Depends: R (>= 2.13.0), EDASeq, DESeq, limma, qvalue Imports: edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots, corrplot, vsn, brew, rjson, log4r Suggests: BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, MADAM, survcomp, VennDiagram, knitr, zoo, RUnit Enhances: parallel, TCC License: GPL (>= 3) MD5sum: 0f84693b38eb618481198040bbd1d5b8 NeedsCompilation: no Package: methVisual Version: 1.16.0 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) MD5sum: 2386c88681d96a4d05827057111760fe NeedsCompilation: no Package: methyAnalysis Version: 1.6.0 Depends: R (>= 2.10), grid, IRanges, GenomicRanges, Biobase (>= 2.5.5), org.Hs.eg.db Imports: lumi, methylumi, Gviz, genoset, GenomicRanges, IRanges, rtracklayer, GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 3cb1d1cda65451b259b95d1fb52e42b3 NeedsCompilation: no Package: methylMnM Version: 1.2.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 75115b462e7c000a14681c9a7681bc43 NeedsCompilation: yes Package: MethylSeekR Version: 1.4.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) MD5sum: f510f93a38c723eff3e886411ce8a2c3 NeedsCompilation: no Package: methylumi Version: 2.10.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, minfi Imports: Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, BiocGenerics, illuminaio Suggests: lumi, lattice, limma, xtable, IlluminaHumanMethylation27k.db (>= 1.4.4), IlluminaHumanMethylation450k.db, SQN, GenomicRanges, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, FDb.InfiniumMethylation.hg19, TCGAMethylation450k, TxDb.Hsapiens.UCSC.hg19.knownGene, IlluminaHumanMethylation450kanno.ilmn12.hg19, Homo.sapiens, knitr License: GPL-2 MD5sum: 1f7ed387a48450a9af495e7f86e67f91 NeedsCompilation: no Package: Mfuzz Version: 2.22.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 27136672cce9305d804af6e31ffea8a5 NeedsCompilation: no Package: mgsa Version: 1.12.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db License: Artistic-2.0 MD5sum: 9e405d0e391840227fcdec7aa69a7b7b NeedsCompilation: yes Package: MiChip Version: 1.18.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: cb308f5fbc8c360180adf140caae017a NeedsCompilation: no Package: microRNA Version: 1.22.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) Suggests: Biostrings (>= 2.11.32) Enhances: Rlibstree License: Artistic-2.0 MD5sum: 69b29179235b0bc39f09ecf5fcfd0efb NeedsCompilation: no Package: MIMOSA Version: 1.0.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, ggplot2, reshape, plyr, Biobase, MASS, testthat, Rcpp LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: Artistic-2.0 MD5sum: c4c9da317d0c3f2fd6525eaa4c7a707f NeedsCompilation: yes Package: MineICA Version: 1.4.0 Depends: R (>= 2.10), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE, methods Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX Enhances: doMC License: GPL-2 MD5sum: c5e38e9c8c5d1151008f7225a852f244 NeedsCompilation: no Package: minet Version: 3.20.2 Depends: infotheo License: CC BY-NC-SA 3.0 MD5sum: 98eab6caec45c4613e0bb44118eebfde NeedsCompilation: yes Package: minfi Version: 1.10.2 Depends: methods, BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), lattice, GenomicRanges, Biostrings, utils, bumphunter (>= 1.1.9) Imports: IRanges, beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, illuminaio, matrixStats, mclust, genefilter, nlme, reshape Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, minfiData (>= 0.4.1), quadprog, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest License: Artistic-2.0 MD5sum: 39a1bef35b9a61b975f917aadbc788ac NeedsCompilation: no Package: MinimumDistance Version: 1.8.1 Depends: R (>= 3.01) Imports: methods, DNAcopy, utils, msm, lattice, BiocGenerics, VanillaICE (>= 1.26.1), ff, Biobase (>= 2.23.6), foreach, oligoClasses (>= 1.24.0), IRanges, GenomicRanges, matrixStats Suggests: human610quadv1bCrlmm (>= 1.0.3), SNPchip, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 162db1bd851ada3b00bbe8d3222116f7 NeedsCompilation: no Package: MiPP Version: 1.36.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: c6adfca178c3c2d4793095cf9685e20c NeedsCompilation: no Package: MiRaGE Version: 1.6.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: AnnotationDbi, BiocGenerics Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 5162bd925fc487028e120e34567f5486 NeedsCompilation: no Package: miRNApath Version: 1.24.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 5f3371c65d6555f512e52aae1a18bdfa NeedsCompilation: no Package: Mirsynergy Version: 1.0.1 Depends: R (>= 3.0.2), igraph, ggplot2 Imports: graphics, grDevices, gridExtra, Matrix, parallel, RColorBrewer, reshape, scales, utils Suggests: glmnet, RUnit, BiocGenerics, knitr License: GPL-2 MD5sum: 09642ed746eee1e730d0b68419b63fd5 NeedsCompilation: no Package: mitoODE Version: 1.2.0 Depends: R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata, KernSmooth License: LGPL MD5sum: 9d07cffe8fffff70efc1c7be778fb1bf NeedsCompilation: yes Package: MLInterfaces Version: 1.44.1 Depends: R (>= 2.9), Biobase, MASS, methods, genefilter, rpart, rda, annotate, cluster, sfsmisc Imports: mboost, gdata, pls Suggests: class, e1071, ipred, randomForest, gpls, pamr, rpart, MASS, nnet, ALL, gbm, mlbench, hgu95av2.db, som, RColorBrewer, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, gbm, mboost, sfsmisc, party Enhances: parallel License: LGPL MD5sum: e322578f8bf8d1caf569db9f010c9ca6 NeedsCompilation: no Package: MLP Version: 1.12.0 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: 3b1d0ecf675857bc2abacf81a48a6c99 NeedsCompilation: no Package: MLSeq Version: 1.0.0 Depends: R (>= 3.0.0), caret, DESeq2, Biobase, limma, randomForest, edgeR Imports: methods Suggests: knitr, e1071, kernlab, earth, ellipse, fastICA, gam, ipred, klaR, MASS, mda, mgcv, mlbench, nnet, party, pls, pROC, proxy, RANN, spls, affy License: GPL (>= 2) MD5sum: 97295040cf3408bdbd10b00c788eacb9 NeedsCompilation: no Package: MMDiff Version: 1.4.1 Depends: R (>= 2.14.0),GenomicRanges,parallel,DiffBind,GMD,Rsamtools Imports: GenomicRanges,IRanges,Biobase Suggests: MMDiffBamSubset License: Artistic-2.0 MD5sum: 717f5e98ec12d22a48b272114eb6c645 NeedsCompilation: no Package: mmnet Version: 1.2.2 Depends: R (>= 2.14), igraph, biom Imports: Biobase, RJSONIO, stringr, reshape2, ggplot2, KEGGREST, plyr, XML, RCurl, flexmix, Matrix, methods, tools Suggests: RCytoscape, graph, knitr License: GPL (>= 2) MD5sum: 97646ebce8c97a638d4b8333fee352d3 NeedsCompilation: no Package: MmPalateMiRNA Version: 1.14.0 Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod, lattice, vsn Imports: limma, lattice, Biobase Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra License: GPL-3 MD5sum: 63f3690037e37209dddc21055f4ca128 NeedsCompilation: no Package: mosaics Version: 1.12.2 Depends: R (>= 2.11.1), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 0b3ad58ae78599cf22de92289952ced4 NeedsCompilation: yes Package: MotifDb Version: 1.6.0 Depends: R (>= 2.15.0), methods, IRanges, Biostrings Imports: BiocGenerics, rtracklayer Suggests: RUnit, MotIV, seqLogo License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: 1a39c1a781ff345802603d94e8f4a0e3 NeedsCompilation: no Package: motifRG Version: 1.8.0 Depends: R (>= 2.15), Biostrings (>= 2.26), IRanges, seqLogo, parallel, methods, grid, graphics, BSgenome, XVector, BSgenome.Hsapiens.UCSC.hg19 Imports: Biostrings,IRanges,seqLogo,parallel,methods,grid,graphics,XVector License: Artistic-2.0 MD5sum: 74a1930f289429c14bfc7d05fb0d235f NeedsCompilation: no Package: motifStack Version: 1.8.1 Depends: R (>= 2.15.1), methods, grImport, grid, MotIV, ade4 Imports: XML Suggests: RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle License: GPL (>= 2) MD5sum: 6e320167b1c573ef3012c0b2076a8e46 NeedsCompilation: no Package: MotIV Version: 1.20.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.0) Imports: graphics, grid, methods, IRanges (>= 1.13.5), Biostrings (>= 1.24.0), lattice, rGADEM, stats, utils Suggests: rtracklayer License: GPL-2 MD5sum: 82c2c6e1fa6b0d89e7e97cbac1ff7f85 NeedsCompilation: yes Package: msmsEDA Version: 1.2.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: 951dfdaefe80f475952b4d96650f11a9 NeedsCompilation: no Package: msmsTests Version: 1.2.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue License: GPL-2 MD5sum: f2c674f8429b710d61c6174960a7dcf8 NeedsCompilation: no Package: MSnbase Version: 1.12.1 Depends: R (>= 3.1), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), ggplot2, mzR Imports: plyr, IRanges, preprocessCore, vsn, grid, reshape2, stats4, affy, impute, pcaMethods, mzID (>= 1.1.5) Suggests: testthat, zoo, knitr (>= 1.1.0), rols, Rdisop, pRolocdata (>= 1.0.7), msdata Enhances: foreach, doMC, parallel License: Artistic-2.0 MD5sum: 4069b237bed56e828b61ceb4c4afdebb NeedsCompilation: no Package: MSstats Version: 2.2.0 Depends: R (>= 3.0), Rcpp, MSnbase, reshape Imports: lme4,marray,limma,gplots,ggplot2, preprocessCore License: Artistic-2.0 MD5sum: 542fd8ddb2a38d272c795096101f2664 NeedsCompilation: no Package: Mulcom Version: 1.14.1 Depends: R (>= 2.10), fields, Biobase Imports: graphics, grDevices, stats, methods License: GPL-2 MD5sum: 7225a4ee43de2d072ef7e0565afc58b8 NeedsCompilation: yes Package: multiscan Version: 1.24.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: 548b3d34c8d057670e6bd069c8882851 NeedsCompilation: yes Package: multtest Version: 2.20.0 Depends: R (>= 2.10), methods, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: ae02ec8b6692f360018bca4fe9dc3550 NeedsCompilation: yes Package: MVCClass Version: 1.38.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 476d1d9b58a2f4f4fc8d24dadc1b5193 NeedsCompilation: no Package: mzID Version: 1.2.1 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators Suggests: knitr License: GPL (>= 2) MD5sum: b52d9e67b16a55ee42d4473ea223a124 NeedsCompilation: no Package: mzR Version: 1.10.8 Depends: Rcpp (>= 0.10.1), methods, utils Imports: Biobase LinkingTo: Rcpp Suggests: msdata (>= 0.1.9), RUnit, faahKO License: Artistic-2.0 MD5sum: 1a367557305080fb59fb328ad3c9727e NeedsCompilation: yes Package: NarrowPeaks Version: 1.8.0 Depends: R (>= 2.10.0), splines Imports: GenomicRanges, IRanges, fda, CSAR Suggests: rtracklayer, GenomicRanges, CSAR, BiocStyle License: Artistic-2.0 MD5sum: f0e7ed15fdedf299d51f170983dea563 NeedsCompilation: yes Package: ncdfFlow Version: 2.10.30 Depends: R (>= 2.14.0), flowCore, flowViz Imports: Biobase,flowCore,flowViz,methods,zlibbioc Suggests: testthat License: Artistic-2.0 MD5sum: f5f3055111c904bcea7a76be35493ebb NeedsCompilation: yes Package: NCIgraph Version: 1.12.0 Depends: graph, R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCytoscape, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 MD5sum: 25bb25f6cc57566e34aaac4a4d74768a NeedsCompilation: no Package: neaGUI Version: 1.2.0 Depends: tcltk Imports: hwriter Suggests: AnnotationDbi, org.Hs.eg.db, KEGG.db, GO.db, reactome.db, RUnit, GOstats,hwriter License: GPL-2 MD5sum: dca2a7fecf364a173a714454c1cd9c3b NeedsCompilation: no Package: nem Version: 2.38.0 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), plotrix, limma, cluster (>= 1.11), statmod, Hmisc, Rgraphviz Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz Suggests: Biobase (>= 1.10) Enhances: doMC, Rglpk License: GPL (>= 2) MD5sum: 316a9773958ed128eebdb81e2724a571 NeedsCompilation: yes Package: NetPathMiner Version: 1.0.4 Depends: R (>= 3.0.2), igraph (>= 0.6) Suggests: rBiopaxParser (>= 2.1), RCurl, RCytoscape License: GPL (>= 2) MD5sum: 18f473abdb8a3fa73980df872db54fbe NeedsCompilation: yes Package: netresponse Version: 1.16.0 Depends: R (>= 2.15.1), dmt, igraph, infotheo, ggplot2, graph, mclust, methods, minet, parallel, qvalue, RColorBrewer, reshape, Rgraphviz License: GPL (>= 2) MD5sum: f789559fb3f3abb8808ab5f9d7000d93 NeedsCompilation: yes Package: NetSAM Version: 1.4.0 Depends: R (>= 2.15.1), methods, igraph (>= 0.6-1), seriation (>= 1.0-6), graph (>= 1.34.0) Imports: methods Suggests: RUnit, BiocGenerics License: LGPL MD5sum: 7fcbc0c3a987cea9dcd47eb13e555beb NeedsCompilation: no Package: networkBMA Version: 1.6.0 Depends: R (>= 2.15.0), stats, utils, BMA, Rcpp (>= 0.10.3), RcppArmadillo (>= 0.3.810.2), RcppEigen (>= 0.3.1.2.1) LinkingTo: Rcpp, RcppArmadillo, RcppEigen License: GPL (>= 2) MD5sum: 30c61a09ff8913a1b5f7ffb69a901f60 NeedsCompilation: yes Package: nnNorm Version: 2.28.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 9bb405ecd5d96c47e14836272a00a578 NeedsCompilation: no Package: NOISeq Version: 2.6.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1) License: Artistic-2.0 MD5sum: ef00323ece7de61a420fd2cb221fe03f NeedsCompilation: no Package: nondetects Version: 1.0.0 Depends: R (>= 3.0.2), Biobase (>= 2.22.0) Imports: utils, methods, HTqPCR (>= 1.16.0) Suggests: BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) License: GPL (>= 2) MD5sum: 0fcb467c97b167f15b9184ac77ef4431 NeedsCompilation: no Package: NormqPCR Version: 1.10.2 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: dbd3cf88cf3f18afd91b2558db429a23 NeedsCompilation: no Package: npGSEA Version: 1.0.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 6284687ede7a2c47421823e5cbcc2142 NeedsCompilation: no Package: NTW Version: 1.14.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: 08ea38c2466ded6c25ad50b513d54bd7 NeedsCompilation: no Package: nucleR Version: 1.12.0 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) MD5sum: 067dda11615822783cfa34cba5f605d5 NeedsCompilation: no Package: nudge Version: 1.30.0 Imports: stats License: GPL-2 MD5sum: fb12d11c3677ed7610062d1a04d7f9a1 NeedsCompilation: no Package: NuPoP Version: 1.14.1 Depends: R (>= 2.10) License: GPL-2 MD5sum: b6568a8fe3be5202df2993f1257f9b87 NeedsCompilation: yes Package: occugene Version: 1.24.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: c4a26d080d6975b7e95bc16003a2b07f NeedsCompilation: no Package: OCplus Version: 1.38.0 Depends: R (>= 2.1.0), akima Imports: multtest (>= 1.7.3), graphics, grDevices, stats License: LGPL MD5sum: 880bfae9a50208b62caa5e6d0e5f4fc9 NeedsCompilation: no Package: oligo Version: 1.28.3 Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.24.0), Biobase (>= 2.17.8), Biostrings (>= 2.25.12) Imports: affyio (>= 1.25.0), affxparser (>= 1.29.11), BiocGenerics (>= 0.3.2), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore (>= 1.19.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, RUnit Enhances: ff, doMC, doMPI License: LGPL (>= 2) MD5sum: 97e95000d334f276faff240274d05733 NeedsCompilation: yes Package: oligoClasses Version: 1.26.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 1.13.30), GenomicRanges, Biostrings (>= 2.23.6), affyio (>= 1.23.2), ff, foreach, BiocInstaller, utils Suggests: RSQLite, hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), crlmm, SNPchip, VanillaICE, RUnit, human370v1cCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 648ce3fe7d6af5ccdb31507beb3d5234 NeedsCompilation: no Package: OLIN Version: 1.42.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 62248b41a62daa8717fae0df3ca167ec NeedsCompilation: no Package: OLINgui Version: 1.38.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: 522ff8ba913bda0cd796105185410944 NeedsCompilation: no Package: omicade4 Version: 1.4.4 Depends: R (>= 3.0.0), ade4 Imports: made4 Suggests: BiocStyle License: GPL-2 MD5sum: 00616599a08c012f58dcf87fd3c62d77 NeedsCompilation: no Package: OmicCircos Version: 1.2.0 Depends: R (>= 2.14.0),methods,GenomicRanges Suggests: knitr License: GPL-2 MD5sum: ba5505b5a55b46dd2d38f3f997678d50 NeedsCompilation: no Package: oneChannelGUI Version: 1.30.6 Depends: Biobase, affylmGUI, tkrplot, tkWidgets, IRanges, Rsamtools (>= 1.13.1), Biostrings, siggenes, chimera Suggests: annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno, chipseq, BSgenome, Rgraphviz, affy ,annaffy, affyPLM, multtest, ssize, sizepower, RankProd, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, edgeR, metaArray, MergeMaid, biomaRt, GenomeGraphs,AffyCompatible, rtracklayer, Genominator, EDASeq, limma, DESeq, DEXSeq, goseq, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, ragene10sttranscriptcluster.db, GOstats, AnnotationDbi, preprocessCore, baySeq, HuExExonProbesetLocation, MoExExonProbesetLocation, RaExExonProbesetLocation, snow, RmiR, RmiR.Hs.miRNA, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn4, R.utils, cummeRbund License: Artistic-2.0 MD5sum: 4890ff4c88aafb986420a5799f03c8bb NeedsCompilation: no Package: ontoCAT Version: 1.16.0 Depends: rJava, methods License: Apache License 2.0 MD5sum: 47ad7fa0c1bf2863a3fe186cd0f39e92 NeedsCompilation: no Package: openCyto Version: 1.2.11 Depends: methods,flowWorkspace Imports: Biobase,gtools,flowCore,flowViz,flowStats,flowClust,MASS,clue,plyr,RBGL,Rgraphviz,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils Suggests: flowWorkspaceData, knitr, testthat, utils, tools License: Artistic-2.0 MD5sum: 9d3cf2d35b07606326c7fc61d3db463c NeedsCompilation: yes Package: OrderedList Version: 1.36.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2), methods Imports: Biobase, graphics, methods, stats, twilight License: GPL (>= 2) MD5sum: 7377463b72f2385c003a0799426a3c96 NeedsCompilation: no Package: OrganismDbi Version: 1.6.0 Depends: R (>= 2.14.0), methods, AnnotationDbi (>= 1.16.10), GenomicFeatures Imports: BiocGenerics, graph, RBGL, AnnotationDbi Suggests: Homo.sapiens, Rattus.norvegicus, RUnit License: Artistic-2.0 MD5sum: 8f6a468d2edc730f5bd8d276bf793495 NeedsCompilation: no Package: OSAT Version: 1.12.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 72d97d1427b8f3a69fe1510e64cd52b3 NeedsCompilation: no Package: OTUbase Version: 1.14.0 Depends: R (>= 2.9.0), methods, ShortRead (>= 1.4.0), Biobase, vegan Imports: Biostrings, ShortRead, IRanges License: Artistic-2.0 MD5sum: 8a51a48aebad266bddbecfe1d9848f8a NeedsCompilation: no Package: OutlierD Version: 1.28.0 Depends: R (>= 2.3.0), Biobase, quantreg License: GPL (>= 2) MD5sum: 03be721293e0f46a35ebecb22799b2b2 NeedsCompilation: no Package: PADOG Version: 1.6.0 Depends: R (>= 2.14.0), KEGGdzPathwaysGEO, graphics, limma, AnnotationDbi, Biobase, methods, nlme, GSA,KEGG.db Imports: graphics, limma, hgu133plus2.db, hgu133a.db, KEGG.db, AnnotationDbi, Biobase, methods, nlme Suggests: parallel License: GPL (>= 2) MD5sum: 13213849ea498cf07dd7f03c8cc9d12d NeedsCompilation: no Package: paircompviz Version: 1.2.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) MD5sum: d41a7c7bd96306e94a799c3a65c7dd50 NeedsCompilation: no Package: PAnnBuilder Version: 1.28.0 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) MD5sum: 5c2a83260b694b8c7f5966cfdffbbcf0 NeedsCompilation: no Package: panp Version: 1.34.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) MD5sum: 70a3cac1fdeaf217ed81bc7f2d8fd85a NeedsCompilation: no Package: PANR Version: 1.10.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils Suggests: snow, RedeR License: Artistic-2.0 MD5sum: 7a72ed7515c009558aa51f8ced3e72b7 NeedsCompilation: no Package: PAPi Version: 1.4.0 Depends: R (>= 2.15.2), svDialogs, KEGGREST License: GPL (>= 2) MD5sum: 77a2783167d32633c26a4fb105c958cf NeedsCompilation: no Package: parody Version: 1.22.0 Depends: R (>= 2.5.0), methods, tools, utils License: Artistic-2.0 MD5sum: 3add047e6b3970d909713e84d823e1ee NeedsCompilation: no Package: pathifier Version: 1.2.0 Imports: R.oo, princurve License: Artistic-1.0 MD5sum: 734bd61840e337ce10667ef8099a70da NeedsCompilation: no Package: PathNet Version: 1.4.0 Depends: R (>= 1.14.0) Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 MD5sum: a3efb0ef754da81637034517b7e9e029 NeedsCompilation: no Package: pathRender Version: 1.32.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods Suggests: ALL, hgu95av2.db License: LGPL MD5sum: 25359ee768e2ae2946c0d4a6112cef13 NeedsCompilation: no Package: pathview Version: 1.4.2 Depends: R (>= 2.10), KEGGgraph, org.Hs.eg.db Imports: Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: c6a0b623597dfd981141d36286828616 NeedsCompilation: no Package: pcaGoPromoter Version: 1.8.0 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) MD5sum: dcbef8ba8ba2dd933a743a6e89c8718c NeedsCompilation: no Package: pcaMethods Version: 1.54.0 Depends: Biobase, methods, Rcpp (>= 0.8.7) Imports: BiocGenerics, MASS LinkingTo: Rcpp Suggests: matrixStats, lattice License: GPL (>= 3) MD5sum: ba338a68efd8a6f0b17cf645c7c419ba NeedsCompilation: yes Package: pcot2 Version: 1.32.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800.db, KEGG.db, mvtnorm License: GPL (>= 2) MD5sum: 626663ca7904937b54c7bdd3a7c835ba NeedsCompilation: no Package: PCpheno Version: 1.26.0 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 MD5sum: b79e6ca15d0393ce85e96cdbc1301cb9 NeedsCompilation: no Package: pdInfoBuilder Version: 1.28.0 Depends: R (>= 2.15.0), methods, Biobase (>= 2.17.7), RSQLite (>= 0.11.1), affxparser (>= 1.29.12), oligo (>= 1.27.3) Imports: Biostrings (>= 2.25.12), IRanges (>= 1.15.44) License: Artistic-2.0 MD5sum: 14ad17916ac808214629638c4301e3fa NeedsCompilation: yes Package: pdmclass Version: 1.36.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda License: Artistic-2.0 MD5sum: 5d74479bc65653dc762b2a8a8e8907cf NeedsCompilation: no Package: PECA Version: 1.0.0 Imports: limma, affy, genefilter, preprocessCore Suggests: SpikeIn, ROCR, multtest License: GPL (>= 2) MD5sum: 5abab331654df29061d298b9ff71d9cc NeedsCompilation: no Package: PGSEA Version: 1.38.0 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 MD5sum: ae76c1cdfeb3e419fd624720296f916d NeedsCompilation: no Package: phenoDist Version: 1.12.0 Depends: R (>= 2.9.0), imageHTS, e1071 Suggests: GOstats, MASS License: LGPL-2.1 MD5sum: bc367b7913ad96b06ebd28355d9209dc NeedsCompilation: no Package: phenoTest Version: 1.12.0 Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, gridExtra Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR, ellipse Suggests: GSEABase, KEGG.db, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: 21312a475007fc8b571eea828d4ccaf7 NeedsCompilation: no Package: PhenStat Version: 1.2.0 Depends: R (>= 2.3.0) Imports: methods, car, nlme, nortest, vcd, limma Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: 64b0018fd4e37038a1c33b094f598f79 NeedsCompilation: no Package: phyloseq Version: 1.8.2 Depends: R (>= 3.0.0) Imports: ade4 (>= 1.6.2), ape (>= 3.1.1), biom (>= 0.3.9), Biostrings (>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.2), DESeq2 (>= 1.4.0), foreach (>= 1.4.2), ggplot2 (>= 1.0.0), igraph (>= 0.6.5.2), methods (>= 3.0.0), multtest (>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.2.3), vegan (>= 2.0.10) Suggests: genefilter (>= 1.42.0), testthat (>= 0.7.1), knitr (>= 1.3) Enhances: doParallel (>= 1.0.1) License: AGPL-3 MD5sum: fc4df3319bf008f626cea43f2af537f2 NeedsCompilation: no Package: piano Version: 1.4.2 Depends: R (>= 2.14.0) Imports: Biobase, gplots, igraph, relations, marray Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall License: GPL (>= 2) MD5sum: 98590cb8e3c549b825b3a5093b6bc8a5 NeedsCompilation: no Package: pickgene Version: 1.36.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: c36bb21cdb0b5539acbb126e0bc93632 NeedsCompilation: no Package: PICS Version: 2.8.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.1.3) Imports: methods, stats4, IRanges, GenomicRanges, graphics, grDevices, stats, Rsamtools, GenomicAlignments Suggests: ShortRead, rtracklayer, parallel License: Artistic-2.0 MD5sum: 2d6043422098fa67a64821284f7f2c87 NeedsCompilation: yes Package: PING Version: 2.8.0 Depends: R(>= 2.15.0), chipseq, IRanges, GenomicRanges Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 MD5sum: e7ff11f513b292202db7422d5b595d80 NeedsCompilation: yes Package: pint Version: 1.16.0 Depends: mvtnorm, methods, graphics, Matrix, dmt License: BSD_2_clause + file LICENSE MD5sum: 250b9c41435ec5bd4c21c6e3afe12bbb NeedsCompilation: no Package: pkgDepTools Version: 1.30.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl, BiocInstaller License: GPL-2 MD5sum: 21a0c9612651e1c6bbe95c0459046d1b NeedsCompilation: no Package: plateCore Version: 1.22.1 Depends: R (>= 2.10), flowCore, flowViz, lattice, latticeExtra Imports: Biobase, flowCore, graphics, grDevices, lattice, MASS, methods, robustbase, stats, utils, flowStats Suggests: gplots License: Artistic-2.0 MD5sum: e53852ea41db9ea50cd85ec194bfc94c NeedsCompilation: no Package: plethy Version: 1.2.2 Depends: R (>= 3.1.0), methods Imports: Streamer, DBI, RSQLite, IRanges, reshape2, plyr, batch, RColorBrewer Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 167a1756b805fab2bcc22c6fd7616696 NeedsCompilation: no Package: plgem Version: 1.36.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), MASS Imports: utils License: GPL-2 MD5sum: ff3b3ff93a227b941b274381901b7667 NeedsCompilation: no Package: plier Version: 1.34.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: 209d7b32bc95ae09970c4e234df2c94a NeedsCompilation: yes Package: PLPE Version: 1.24.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: 03f85a5cb38138ee02c8c57b92b43e4d NeedsCompilation: no Package: plrs Version: 1.4.0 Depends: R (>= 2.10), Biobase Imports: BiocGenerics, CGHbase, graphics, grDevices, ic.infer, marray, methods, quadprog, Rcsdp, stats, stats4, utils Suggests: mvtnorm, methods License: GPL (>= 2.0) MD5sum: d901ee3f8121188cc4963cfd7e5b5a45 NeedsCompilation: no Package: plw Version: 1.24.0 Depends: R (>= 2.10), affy (>= 1.23.4) Imports: MASS, affy, graphics, splines, stats Suggests: limma License: GPL-2 MD5sum: abc3ea97703ddb63e4364695c12e6a69 NeedsCompilation: yes Package: ppiStats Version: 1.30.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.19) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable License: Artistic-2.0 MD5sum: 85fcb75a6491708bde991e4fadbad62d NeedsCompilation: no Package: prada Version: 1.40.0 Depends: R (>= 2.10), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, BiocGenerics, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, stats4, utils Suggests: cellHTS, tcltk License: LGPL MD5sum: 87b43b5558cf3ff2217f175c75875e01 NeedsCompilation: yes Package: prebs Version: 1.4.0 Depends: R (>= 2.14.0), GenomicAlignments, affy Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 MD5sum: 6ff8432b9e11854ccd93d870ed927e95 NeedsCompilation: no Package: PREDA Version: 1.10.0 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 MD5sum: 064808d9e45fce1acfd86512039e2f3e NeedsCompilation: no Package: predictionet Version: 1.10.0 Depends: igraph, catnet Imports: penalized, RBGL, MASS Suggests: network, minet, knitr License: Artistic-2.0 MD5sum: 7a2a3254d02e3177ce85b45c00581fa2 NeedsCompilation: yes Package: preprocessCore Version: 1.26.1 Depends: methods Imports: stats License: LGPL (>= 2) MD5sum: bfac63ebbee13b22849ea37fd56657a6 NeedsCompilation: yes Package: PROcess Version: 1.40.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 MD5sum: 8a84dad6a306e808ec6c2a6e246928a5 NeedsCompilation: no Package: procoil Version: 1.14.0 Depends: R (>= 2.12.0) Imports: methods, stats, graphics Suggests: Biostrings License: GPL (>= 2) MD5sum: aff9adf11c3fdb601fb46029109c262f NeedsCompilation: no Package: ProCoNA Version: 1.2.0 Depends: R (>= 2.10), methods, WGCNA, MSnbase Imports: BiocGenerics, GOstats Suggests: RUnit License: GPL (>= 2) MD5sum: de009234b762aa33bf894ba2f61179b3 NeedsCompilation: no Package: pRoloc Version: 1.4.0 Depends: R (>= 2.15), MSnbase (>= 1.7.23), MLInterfaces (>= 1.37.1), methods, Rcpp (>= 0.10.3), BiocParallel Imports: mclust (>= 4.3), MSBVAR, caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, BiocGenerics, stats4, RColorBrewer, scales, MASS, knitr LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, pRolocdata, roxygen2, synapter, xtable License: GPL-2 MD5sum: ae22843e21edb36bd4c4d1c211f96fb0 NeedsCompilation: yes Package: PROMISE Version: 1.16.0 Depends: R (>= 2.11.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) MD5sum: 6e1774b297793dc9a6a7f47f8a5635c1 NeedsCompilation: no Package: prot2D Version: 1.2.0 Depends: R (>= 2.15),fdrtool,st,samr,Biobase,limma,Mulcom,impute,MASS,qvalue Suggests: made4,affy License: GPL (>= 2) MD5sum: dff0e37ebfd565ce468754d90226fb45 NeedsCompilation: no Package: proteinProfiles Version: 1.4.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 MD5sum: 52a9026b570904b44ed467df7b439508 NeedsCompilation: no Package: PSICQUIC Version: 1.2.1 Depends: R (>= 2.15.0), methods, IRanges, biomaRt, BiocGenerics Imports: RCurl Suggests: org.Hs.eg.db License: Apache License 2.0 MD5sum: 736ffc97b3277ceaa21df9e1ea464954 NeedsCompilation: no Package: puma Version: 3.6.0 Depends: R (>= 3.0), Biobase (>= 2.5.5), affy (>= 1.41.3), graphics, grDevices, methods, stats, utils, mclust, oligo, Imports: Biobase (>= 2.5.5), affy (>= 1.41.3), affyio Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL MD5sum: ac1613e96d99ef958df382cb1afd511d NeedsCompilation: yes Package: pvac Version: 1.12.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: 3f7c972b0f8a4ab4a09a8cf9ed63e17c NeedsCompilation: no Package: pvca Version: 1.4.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: 5b3e72ae74e99380b60900181a23a97f NeedsCompilation: no Package: PWMEnrich Version: 3.6.1 Depends: methods, grid, BiocGenerics, Biostrings, Imports: seqLogo, gdata, evd Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel License: LGPL (>= 2) MD5sum: 5a005dd3ebd0655f3add0945fd9af424 NeedsCompilation: no Package: qcmetrics Version: 1.2.0 Depends: R (>= 2.10) Imports: Biobase, methods, knitr, tools, Nozzle.R1, xtable, pander Suggests: affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX, RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf License: GPL-2 MD5sum: c4df8195ba757745fa987af94f7ab866 NeedsCompilation: no Package: QDNAseq Version: 1.0.5 Depends: R (>= 2.15.0) Imports: graphics, methods, stats, utils, matrixStats (>= 0.9.4), R.utils (>= 1.28.4), Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), Rsamtools (>= 1.10.0) Suggests: R.cache (>= 0.9.0), digest, snowfall, BSgenome, GenomeInfoDb, GenomicRanges License: GPL MD5sum: 8ade2fbf3a766560a6727fcc5be004c0 NeedsCompilation: no Package: qpcrNorm Version: 1.22.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) MD5sum: f2e78f88a4dd421ce606a5790e343610 NeedsCompilation: no Package: qpgraph Version: 1.20.2 Depends: R (>= 3.0.0) Imports: methods, parallel, Matrix (>= 1.0), annotate, graph (>= 1.41.2), Biobase, GGBase, AnnotationDbi, mvtnorm, qtl, Rgraphviz Suggests: BiocStyle, genefilter, org.EcK12.eg.db Enhances: rlecuyer, snow, Category, GOstats License: GPL (>= 2) MD5sum: 304dcb639b31acc0f9cb452497696459 NeedsCompilation: yes Package: qrqc Version: 1.18.0 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) MD5sum: 0cab4c8ef66ab85ece1a8b84f67e0e39 NeedsCompilation: yes Package: QUALIFIER Version: 1.8.23 Depends: R (>= 2.14.0),flowCore,flowViz,ncdfFlow,flowWorkspace, data.table,reshape Imports: MASS,hwriter,lattice,stats4,flowCore,flowViz,methods,flowWorkspace,latticeExtra,grDevices,tools, Biobase,XML Suggests: RSVGTipsDevice License: Artistic-2.0 MD5sum: ca7b57689e76b7d4c26b0f5a1b31b0f4 NeedsCompilation: no Package: quantsmooth Version: 1.30.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 MD5sum: 0c92ecf3ae8c34d5cd0717499422d001 NeedsCompilation: no Package: QuasR Version: 1.4.2 Depends: parallel, GenomicRanges (>= 1.13.3), Rbowtie Imports: methods, zlibbioc, BiocGenerics, IRanges, BiocInstaller, Biobase, Biostrings, GenomicRanges, BSgenome, Rsamtools (>= 1.13.1), GenomicFeatures, ShortRead (>= 1.19.1), GenomicAlignments LinkingTo: Rsamtools Suggests: Rsamtools, rtracklayer, Gviz, RUnit, BiocStyle License: GPL-2 MD5sum: 3603366a7415b37fc82eab1cc2f56589 NeedsCompilation: yes Package: qusage Version: 1.4.0 Depends: R (>= 2.10), limma (>= 3.14), methods Imports: utils, Biobase License: GPL (>= 2) MD5sum: 0756127f96c0ea93651dd97cc741ee50 NeedsCompilation: no Package: qvalue Version: 1.38.0 Imports: graphics, grDevices, stats, tcltk License: LGPL MD5sum: d3a580ea20b886f5f05a24c5174035cf NeedsCompilation: no Package: r3Cseq Version: 1.10.0 Depends: GenomicRanges,Rsamtools,data.table,rtracklayer,VGAM,qvalue,RColorBrewer,sqldf,methods Suggests: BSgenome.Mmusculus.UCSC.mm9.masked,BSgenome.Hsapiens.UCSC.hg18.masked,BSgenome.Hsapiens.UCSC.hg19.masked License: GPL-3 MD5sum: b5e99276514c1dda8ebf5b155e61c410 NeedsCompilation: no Package: R453Plus1Toolbox Version: 1.14.0 Depends: R (>= 2.12.0), Biobase, Biostrings, GenomicRanges Imports: BiocGenerics (>= 0.1.3), biomaRt, BSgenome, IRanges, XVector, methods, R2HTML, Rsamtools, ShortRead, VariantAnnotation, xtable, tools, TeachingDemos Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 License: LGPL-3 MD5sum: 3c0d780eddfcb6fcc2b81370c86f71d6 NeedsCompilation: yes Package: rama Version: 1.38.0 Depends: R(>= 2.5.0) License: GPL (>= 2) MD5sum: f916fb59cc93f96d639d5d5900b137a2 NeedsCompilation: yes Package: RamiGO Version: 1.10.0 Depends: gsubfn,methods Imports: igraph,RCurl,png,RCytoscape,graph License: Artistic-2.0 MD5sum: 10efbe664ac08bdda8f375264b591916 NeedsCompilation: no Package: randPack Version: 1.10.0 Depends: methods Imports: Biobase License: Artistic-2.0 MD5sum: 81333fea32efbfdd5e7740f2e6397bd7 NeedsCompilation: no Package: RankProd Version: 2.36.0 Depends: R (>= 1.9.0) Imports: graphics License: file LICENSE License_restricts_use: yes MD5sum: b6495bd4649fc45da64ad8250b105046 NeedsCompilation: no Package: Rariant Version: 1.0.0 Depends: R (>= 3.0.2) Imports: IRanges, ggbio, ggplot2, VariantAnnotation, h5vc, exomeCopy, SomaticSignatures, Rsamtools, shiny, GenomicRanges Suggests: h5vcData, testthat, knitr, BiocStyle, biovizBase, optparse License: GPL-3 MD5sum: 47beebbfe1fa433d604d20b045924b06 NeedsCompilation: no Package: RbcBook1 Version: 1.32.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 MD5sum: b895de489e1e0ecb3f27cffe1b41b7a9 NeedsCompilation: no Package: RBGL Version: 1.40.1 Depends: graph, methods Imports: methods Suggests: Rgraphviz, XML License: Artistic-2.0 MD5sum: 9b92ab942e08916c62d40fe42b71ebf0 NeedsCompilation: yes Package: RBioinf Version: 1.24.0 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 MD5sum: a9a14512b58a18274be35a461ce67f26 NeedsCompilation: yes Package: rBiopaxParser Version: 2.2.0 Depends: R (>= 3.0.0), data.table Imports: XML Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL License: GPL (>= 2) MD5sum: 7ca1d9eeef3b55b660a6387f87eeb721 NeedsCompilation: no Package: Rbowtie Version: 1.4.5 Suggests: parallel License: Artistic-1.0 | file LICENSE MD5sum: c0c4caba91563a8e0f067114dce72e55 NeedsCompilation: yes Package: rbsurv Version: 2.22.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) MD5sum: 067f1a0901313da9ec5d541e2139e43a NeedsCompilation: no Package: Rcade Version: 1.6.0 Depends: R (>= 2.14.0), methods, GenomicRanges, baySeq, Rsamtools Imports: graphics, IRanges, rgl Suggests: limma, biomaRt, RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: a235e17714a7b98bc24980812c1b2bb4 NeedsCompilation: no Package: RCASPAR Version: 1.10.0 License: GPL (>= 3) MD5sum: 628986373c826a618bfe0f0afe4a1524 NeedsCompilation: no Package: Rchemcpp Version: 2.2.0 Depends: R (>= 2.15.0) Imports: Rcpp (>= 0.11.1), methods, ChemmineR LinkingTo: Rcpp Suggests: apcluster, kernlab License: GPL (>= 2.1) MD5sum: 2eab5f3431ae6f851548016b0892897a NeedsCompilation: yes Package: RchyOptimyx Version: 2.4.0 Depends: R (>= 2.10) Imports: Rgraphviz, sfsmisc, graphics, methods, graph, grDevices, flowType (>= 2.0.0) Suggests: flowCore License: Artistic-2.0 MD5sum: 0f188ffcfcbc6383bf000b614759db5f NeedsCompilation: yes Package: Rcpi Version: 1.0.2 Imports: RCurl, rjson, rcdk, foreach, doParallel, Biostrings, GOSemSim, ChemmineR, fmcsR Suggests: RUnit, BiocGenerics Enhances: ChemmineOB License: Artistic-2.0 MD5sum: ad0eca2f70a1d5432dbb1a3fb3712716 NeedsCompilation: no Package: RCytoscape Version: 1.14.0 Depends: R (>= 2.14.0), graph (>= 1.31.0), XMLRPC (>= 0.2.4) Imports: methods, XMLRPC, BiocGenerics Suggests: RUnit License: GPL-2 MD5sum: eb08c22f5fdc63eeeadee28bcd5e11b7 NeedsCompilation: no Package: RDAVIDWebService Version: 1.2.0 Depends: R (>= 2.14.1), methods, graph, GOstats, ggplot2 Imports: Category, GO.db, RBGL, rJava Suggests: Rgraphviz License: GPL (>= 2) MD5sum: 73df072f6a592ea242530394ae14063a NeedsCompilation: no Package: Rdisop Version: 1.24.1 Depends: R (>= 2.0.0), RcppClassic LinkingTo: RcppClassic, Rcpp Suggests: RUnit License: GPL-2 MD5sum: 2ac72bd7832d8ace208611a6386146e5 NeedsCompilation: yes Package: RDRToolbox Version: 1.14.0 Depends: R (>= 2.9.0) Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) MD5sum: 7e0fd28b0be4b0c96b0504c52ac67b24 NeedsCompilation: no Package: ReactomePA Version: 1.8.1 Imports: AnnotationDbi, reactome.db, org.Hs.eg.db, DOSE, igraph, graphite Suggests: clusterProfiler, GOSemSim, ChIPseeker, knitr License: GPL-2 MD5sum: e81c2797d8bcf5625b9bc08ea328caf9 NeedsCompilation: no Package: ReadqPCR Version: 1.10.0 Depends: R(>= 2.14.0), Biobase, methods, affy Imports: Biobase Suggests: qpcR License: LGPL-3 MD5sum: e39a6ea2737bc90d617b24b71ac2c522 NeedsCompilation: no Package: reb Version: 1.42.0 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) License: GPL-2 MD5sum: 2aa657fb1f10d8010b0d5e2d4dbaf28b NeedsCompilation: yes Package: RedeR Version: 1.12.9 Depends: R (>= 2.15), methods, igraph Imports: RCurl, XML Suggests: PANR, pvclust License: GPL (>= 2) MD5sum: 2cad007bd71ea666bf67e21d3c33483c NeedsCompilation: no Package: REDseq Version: 1.10.0 Depends: R (>= 2.15.0), BiocGenerics (>= 0.1.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges (>= 1.13.5), multtest, stats, utils License: GPL (>= 2) MD5sum: b3bcddd851316e37b77d548b24dd9150 NeedsCompilation: no Package: RefNet Version: 1.0.4 Depends: R (>= 2.15.0), methods, IRanges, PSICQUIC, AnnotationHub, RCurl Imports: BiocGenerics Suggests: RUnit, BiocStyle, org.Hs.eg.db License: Artistic-2.0 MD5sum: a7811ff69ca6397776d3d68862bff28b NeedsCompilation: no Package: RefPlus Version: 1.34.0 Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM (>= 1.18.0), preprocessCore (>= 1.4.0) Suggests: affydata License: GPL (>= 2) MD5sum: ecde2300c4e3884d0760091d2ecba337 NeedsCompilation: no Package: Repitools Version: 1.10.1 Depends: R (>= 3.0.0), methods, BiocGenerics (>= 0.8.0) Imports: IRanges (>= 1.20.0), GenomicRanges, GenomicAlignments, BSgenome, gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Ringo, aroma.affymetrix, Rsolnp, parallel, Biostrings, Rsamtools, cluster Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18, rtracklayer License: LGPL (>= 2) MD5sum: 1492dff34d67382fd33587ab15a317aa NeedsCompilation: yes Package: ReportingTools Version: 2.4.0 Depends: methods, knitr Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), IRanges, ggplot2, ggbio Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, License: Artistic-2.0 MD5sum: 6bae53b1b4b8a7e210a490840ed57e3a NeedsCompilation: no Package: ReQON Version: 1.10.0 Depends: R (>= 3.0.2), Rsamtools, seqbias Imports: rJava, graphics, stats, utils, grDevices Suggests: BiocStyle License: GPL-2 MD5sum: 9b48ccd475b6462ad8939275c7145dad NeedsCompilation: no Package: Resourcerer Version: 1.38.0 Depends: R (>= 1.9.0), Biobase, AnnotationDbi (>= 1.4.0) Suggests: human.db0, mouse.db0, rat.db0 License: LGPL MD5sum: 53c5f3e4a7b17db7466bdabd86aec5d4 NeedsCompilation: no Package: rfPred Version: 1.2.0 Depends: Rsamtools, GenomicRanges, IRanges, data.table, methods, parallel Suggests: BiocStyle License: GPL (>= 2) MD5sum: 4374eedf7ad41dc1f0e9f08cbf92255d NeedsCompilation: yes Package: rGADEM Version: 2.12.0 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 MD5sum: 4a9468700dfe896dd3cf1a3b760b7a6b NeedsCompilation: yes Package: RGalaxy Version: 1.8.1 Depends: XML, methods, tools, optparse, digest, Imports: BiocGenerics, Biobase, roxygen2 Suggests: RUnit, hgu95av2.db, knitr, formatR, Rserve Enhances: RSclient License: Artistic-2.0 MD5sum: 42c20d72e25098da5d1b1b046fc1998c NeedsCompilation: no Package: Rgraphviz Version: 2.8.1 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL MD5sum: 37ddbd4d31e4203d6124288647f8cadb NeedsCompilation: yes Package: rhdf5 Version: 2.8.0 Depends: methods Imports: zlibbioc Suggests: bit64,BiocStyle License: Artistic-2.0 MD5sum: 33767e9a4bb07c1de12776c3590c3777 NeedsCompilation: yes Package: rHVDM Version: 1.30.0 Depends: R (>= 2.10), R2HTML (>= 1.5), affy (>= 1.23.4), minpack.lm (>= 1.0-5), Biobase (>= 2.5.5) License: GPL-2 MD5sum: eada13f56ec8b4f9dd0fa2200299e916 NeedsCompilation: no Package: Ringo Version: 1.28.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid, lattice Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4 Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 MD5sum: ec5c8731b5ab79a2353acb62d7e96299 NeedsCompilation: yes Package: RIPSeeker Version: 1.4.0 Depends: R (>= 2.15), methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments, rtracklayer Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures License: GPL-2 MD5sum: 3943c4528b51e44105e43f882a15a781 NeedsCompilation: no Package: Risa Version: 1.6.0 Depends: R (>= 2.0.9), Biobase (>= 2.4.0), methods, Rcpp (>= 0.9.13), biocViews, affy Imports: xcms Suggests: faahKO (>= 1.2.11) License: LGPL MD5sum: ad9afaa4f4eee9470a21e406df122ec5 NeedsCompilation: no Package: RLMM Version: 1.26.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: 8b1a3041c8b8af45dd41c8720ba7c26d NeedsCompilation: no Package: Rmagpie Version: 1.20.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) MD5sum: 809356723910e63f94c7ca9644273d58 NeedsCompilation: no Package: RMAPPER Version: 1.14.0 Depends: methods Suggests: RCurl License: Artistic-2.0 MD5sum: 3edbccdfec39be5776bc250df4cc9433 NeedsCompilation: no Package: RMassBank Version: 1.6.0 Depends: Rcpp Imports: XML,RCurl,rjson, rcdk,yaml,mzR,methods Suggests: gplots,RMassBankData, xcms (>= 1.37.1), CAMERA, ontoCAT, RUnit License: Artistic-2.0 MD5sum: 9846557740513ea7c41c0c15111b7ff3 NeedsCompilation: no Package: rMAT Version: 3.14.0 Depends: R(>= 2.9.0), BiocGenerics (>= 0.1.3), IRanges (>= 1.13.10), Biobase (>= 2.15.1), affxparser Imports: stats, methods, BiocGenerics, IRanges, Biobase, affxparser, stats4 Suggests: GenomeGraphs, rtracklayer License: Artistic-2.0 MD5sum: 13a9b4e1d5a13e1c45ed1b52add24db5 NeedsCompilation: yes Package: RmiR Version: 1.20.0 Depends: R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice Imports: DBI, methods, stats Suggests: hgug4112a.db,org.Hs.eg.db License: Artistic-2.0 MD5sum: 8f8df136d1282c00019ed898c0504b1d NeedsCompilation: no Package: RNAinteract Version: 1.12.0 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 MD5sum: 4dce0bdeae427bf7537f38f1941d69a6 NeedsCompilation: no Package: RNAither Version: 2.12.0 Depends: R (>= 2.10), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt, car, splots, methods License: Artistic-2.0 MD5sum: 42b486bc6608bf3b33d10273473aa487 NeedsCompilation: no Package: rnaSeqMap Version: 2.20.0 Depends: R (>= 2.11.0), methods, Biobase, Rsamtools, GenomicAlignments Imports: GenomicRanges , IRanges, edgeR, DESeq, DBI License: GPL-2 MD5sum: 77ef6bc050c7bfd1a77c5207d6f3b346 NeedsCompilation: yes Package: RNASeqPower Version: 1.4.0 License: LGPL (>= 2) MD5sum: 80afff847658fae7a3a030f0c9df2b7b NeedsCompilation: no Package: roar Version: 1.0.0 Depends: R (>= 3.0.1) Imports: GenomicRanges, GenomicAlignments(>= 0.99.4), methods, rtracklayer, IRanges Suggests: RUnit, BiocGenerics, RNAseqData.HNRNPC.bam.chr14 License: GPL-3 MD5sum: af6bfdf2e438952baad06c0409bc406d NeedsCompilation: no Package: ROC Version: 1.40.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase License: Artistic-2.0 MD5sum: edde9a3f4e5a07275f389885283007c7 NeedsCompilation: yes Package: Roleswitch Version: 1.2.0 Depends: R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt, Biostrings, Biobase, DBI Suggests: ggplot2 License: GPL-2 MD5sum: 394e3ba868a3be18c7214a45ceb24ddc NeedsCompilation: no Package: Rolexa Version: 1.20.0 Depends: R (>= 2.9.0), graphics, grDevices, methods, ShortRead Imports: mclust, Biostrings, graphics, grDevices, IRanges, methods, ShortRead, stats Enhances: fork License: GPL-2 MD5sum: b97f51aa173505e3e1e674d72d5e4ac1 NeedsCompilation: no Package: rols Version: 1.6.1 Depends: methods Imports: XML, XMLSchema (>= 0.6.0), SSOAP (>= 0.8.0), Biobase Suggests: xtable, GO.db, knitr (>= 1.1.0), BiocStyle License: GPL-2 MD5sum: 8262fcdb4f9bc6678a481b06d59f58a2 NeedsCompilation: no Package: ROntoTools Version: 1.4.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 20be22821c46d088ea6afcec79964119 NeedsCompilation: no Package: RPA Version: 1.20.01 Depends: R (>= 2.15.0), affy, affydata, methods, parallel License: BSD_2_clause + file LICENSE MD5sum: 9928f480d784f3d11e46add9c37f96c0 NeedsCompilation: no Package: RpsiXML Version: 2.6.0 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 MD5sum: 4eed4f01d66445ba522e96611667b20f NeedsCompilation: no Package: rpx Version: 1.0.1 Depends: methods Imports: XML, RCurl, utils Suggests: MSnbase, Biostrings, BiocStyle, BiocGenerics, RUnit, knitr License: GPL-2 MD5sum: 6dddad3476162756cf20dc163a3bebd9 NeedsCompilation: no Package: rqubic Version: 1.10.0 Depends: methods, Biobase, biclust Imports: Biobase, biclust Suggests: RColorBrewer License: GPL-2 MD5sum: 5dba51e190b10fd86af817dadcbe52cf NeedsCompilation: yes Package: RRHO Version: 1.2.0 Depends: VennDiagram, grid License: GPL-2 MD5sum: 36e3cf7a04952673b3620ddc7a4a8b7b NeedsCompilation: no Package: Rsamtools Version: 1.16.1 Depends: methods, IRanges (>= 1.21.10), GenomicRanges (>= 1.15.11), XVector (>= 0.3.2), Biostrings (>= 2.31.3), GenomeInfoDb(>= 0.99.17) Imports: utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops LinkingTo: IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 | file LICENSE MD5sum: 0876502f73b88f0c47034aefbbafc2d3 NeedsCompilation: yes Package: rsbml Version: 2.22.2 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: 9efc4f012e347edfbbc9d90db5a3d062 NeedsCompilation: yes Package: rSFFreader Version: 0.12.0 Depends: R (>= 2.13.0), BiocGenerics, IRanges (>= 1.21.10), XVector (>= 0.3.2), Biostrings (>= 2.31.3), GenomicRanges, ShortRead (>= 1.15.9), xtable, methods Imports: methods, IRanges, XVector, Biostrings, ShortRead, GenomicRanges, Biobase LinkingTo: IRanges, XVector, Biostrings License: Artistic-2.0 MD5sum: 1355df53257a50d8032c11605c623657 NeedsCompilation: yes Package: Rsubread Version: 1.14.2 License: GPL-3 MD5sum: 6fcf162be4edbdc96d36fd18ff95af29 NeedsCompilation: yes Package: RSVSim Version: 1.4.0 Depends: R (>= 3.0.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, MASS, rtracklayer License: LGPL-3 MD5sum: a7d44a71abd347ddd523fb62ca8274cf NeedsCompilation: no Package: rTANDEM Version: 1.4.0 Depends: XML, Rcpp, data.table (>= 1.8.8) Imports: methods LinkingTo: Rcpp Suggests: biomaRt License: Artistic-1.0 | file LICENSE MD5sum: 63912445a0e93d380e6c2ab32fbcda8d NeedsCompilation: yes Package: RTCA Version: 1.16.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: acc3772bf7d0fdb1b7556741001ef668 NeedsCompilation: no Package: RTN Version: 1.2.7 Depends: R (>= 2.15), methods, igraph Imports: RedeR, minet, snow, limma, data.table, ff, car, IRanges Suggests: HTSanalyzeR, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: ef69c859338b7a0e7a0556f38af5a40b NeedsCompilation: no Package: RTopper Version: 1.10.0 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db License: GPL (>= 3) MD5sum: fef08400d2c86359a1dfb457d5a6395f NeedsCompilation: no Package: rtracklayer Version: 1.24.2 Depends: R (>= 2.10), methods, GenomicRanges (>= 1.15.26) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.7.7), IRanges (>= 1.19.34), XVector (>= 0.1.3), GenomicRanges (>= 1.15.26), Biostrings (>= 2.29.18), BSgenome (>= 1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.13.1), GenomicAlignments, tools LinkingTo: IRanges, XVector 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 MD5sum: 0f1f6fb8785265b84e8964eec9db95b3 NeedsCompilation: yes Package: Rtreemix Version: 1.26.0 Depends: R (>= 2.5.0), methods, graph, Biobase Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL MD5sum: f448d2a625dbc8d4080f30b07eecb147 NeedsCompilation: yes Package: rTRM Version: 1.2.0 Depends: R (>= 2.10), igraph (>= 0.7), RSQLite Imports: AnnotationDbi Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2 License: GPL-3 MD5sum: 0b69533dda5eae04f77f77034998cb62 NeedsCompilation: no Package: rTRMui Version: 1.2.0 Imports: shiny (>= 0.5), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: b5bd1f424fbc7c5fafed72c8ea02de4e NeedsCompilation: no Package: RWebServices Version: 1.28.0 Depends: SJava (>= 0.85), TypeInfo, methods, tools (>= 2.10.0), R (>= 2.5.0) Imports: RCurl, SJava License: file LICENSE License_restricts_use: no MD5sum: 2504b02aefeac395be6dec40805606d5 NeedsCompilation: yes Package: safe Version: 3.4.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, KEGG.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 8c88d3ccf8cdd583773fdcfab5f3111a NeedsCompilation: no Package: sagenhaft Version: 1.34.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, methods, SparseM, stats, utils License: GPL (>= 2) MD5sum: 2abc04eea091fa17d6954077912775b7 NeedsCompilation: no Package: SAGx Version: 1.38.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase, stats4 Suggests: KEGG.db, hu6800.db, MASS License: GPL-3 MD5sum: dbf58a2cb1bacec5bfcd586ae33ca6a1 NeedsCompilation: yes Package: SamSPECTRAL Version: 1.18.0 Depends: R (>= 2.10) Imports: methods License: GPL (>= 2) MD5sum: 583e14f8256f3b196e92df326cf1129e NeedsCompilation: yes Package: sangerseqR Version: 1.0.0 Depends: R (>= 3.0.2), Biostrings Imports: methods Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: c8b5e768ec52710b39977d9438f722db NeedsCompilation: no Package: SANTA Version: 1.4.0 Depends: R (>= 2.14), igraph Imports: Matrix, msm, snow Suggests: RUnit, BiocGenerics, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 3ecd398a129d2236ef8bd08ff0429148 NeedsCompilation: yes Package: sapFinder Version: 1.0.1 Depends: R (>= 3.0.0),rTANDEM (>= 1.3.5) Imports: pheatmap,Rcpp (>= 0.10.6),graphics,grDevices,stats, utils LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: e0d47be78cc335a01f70bb89754a73b8 NeedsCompilation: yes Package: savR Version: 1.2.0 Depends: ggplot2 Imports: methods, reshape2, scales, gridExtra, XML Suggests: Cairo License: AGPL-3 MD5sum: a9f7a5f42e611e5b033fde00b71fce9f NeedsCompilation: no Package: SBMLR Version: 1.60.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: 0bf1e8d5005ddd494fcfc459b20e7ded NeedsCompilation: no Package: SCAN.UPC Version: 2.6.3 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools Suggests: pd.hg.u95a License: MIT MD5sum: 658f40d2e79d3844178c73a15b9850f4 NeedsCompilation: no Package: ScISI Version: 1.36.0 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 MD5sum: 6d1e23327c069c4d8f7a4b73422f96a6 NeedsCompilation: no Package: scsR Version: 1.0.0 Depends: R (>= 2.14.0), methods, BiocGenerics, Biostrings, IRanges, plyr, STRINGdb, tcltk Imports: sqldf, hash, ggplot2, graphics,grDevices, RColorBrewer Suggests: RUnit License: GPL-2 MD5sum: f85f30278a4b9c462a6fb92c6e176d6f NeedsCompilation: no Package: segmentSeq Version: 1.16.0 Depends: R (>= 2.3.0), methods, baySeq (>= 1.15.4), ShortRead, GenomicRanges, IRanges Imports: baySeq, graphics, grDevices, IRanges, methods, utils, GenomicRanges Suggests: snow License: GPL-3 MD5sum: 8197b780736fc0ae9a9cd28f7b040bcb NeedsCompilation: no Package: SeqArray Version: 1.4.0 Depends: gdsfmt (>= 1.0.0) Imports: methods, parallel, Biostrings, GenomicRanges, IRanges, VariantAnnotation Suggests: BiocGenerics, RUnit, Rcpp License: GPL-3 MD5sum: 9380f2001117370ea6bf7a46c6917600 NeedsCompilation: yes Package: seqbias Version: 1.12.0 Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods Imports: zlibbioc LinkingTo: Rsamtools Suggests: Rsamtools, ggplot2 License: LGPL-3 MD5sum: 3c8a969be12a3d9a0af1eab0648d33ae NeedsCompilation: yes Package: seqCNA Version: 1.6.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 036b5ef8cca83e315c6e41d7ceadfecf NeedsCompilation: yes Package: SeqGSEA Version: 1.4.2 Depends: Biobase, doParallel, DESeq Imports: methods, biomaRt Suggests: easyRNASeq, GenomicRanges License: GPL (>= 3) MD5sum: f92f999f90aba338d83d740e1b6a7aa3 NeedsCompilation: no Package: seqLogo Version: 1.30.0 Depends: methods, grid License: LGPL (>= 2) MD5sum: b85a52262827218be7ae0cdf1c1001e3 NeedsCompilation: no Package: SeqVarTools Version: 1.2.0 Depends: SeqArray (>= 1.1.1) Imports: methods, GenomicRanges, IRanges, GWASExactHW Suggests: BiocGenerics, RUnit License: GPL-3 MD5sum: a072d52a1a0ba6c44d028eb2397ed04f NeedsCompilation: no Package: shinyTANDEM Version: 1.2.0 Depends: rTANDEM (>= 1.3.5), shiny, mixtools, methods, xtable License: GPL-3 MD5sum: 83dbaf6d5e975de32bb14a4ec97c7e6b NeedsCompilation: no Package: ShortRead Version: 1.22.0 Depends: BiocGenerics (>= 0.1.0), BiocParallel, Biostrings (>= 2.31.14), Rsamtools (>= 1.13.1), GenomicAlignments (>= 0.99.6) Imports: Biobase, GenomicRanges (>= 1.15.26), IRanges (>= 1.21.22), hwriter, methods, zlibbioc, lattice, latticeExtra, LinkingTo: IRanges, XVector, Biostrings Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi License: Artistic-2.0 MD5sum: 5730295ed8e5c433e52316ac94336dda NeedsCompilation: yes Package: sigaR Version: 1.8.0 Depends: Biobase, CGHbase, methods, mvtnorm, penalized Imports: corpcor (>= 1.6.2), graphics, igraph, marray, MASS, mvtnorm, quadprog, penalized (>= 0.9-39), snowfall, stats License: GPL (>= 2) MD5sum: e16d4be042f528bc4e48bd6c4fb3573f NeedsCompilation: no Package: SigFuge Version: 1.2.0 Depends: R (>= 3.0.2), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: 35b574f1da3829acb26e0513dd09409b NeedsCompilation: no Package: siggenes Version: 1.38.0 Depends: methods, Biobase, multtest, splines, graphics Imports: stats4 Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5) License: LGPL (>= 2) MD5sum: 01c3dafcbcb103173e3c9a653fdae3b3 NeedsCompilation: no Package: sigPathway Version: 1.32.1 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 MD5sum: d47a845f2056d2c86c93512a6fbd4d49 NeedsCompilation: yes Package: SIM Version: 1.34.0 Depends: R (>= 2.4), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: b2cbd3b412af648952881a41df1efcea NeedsCompilation: yes Package: SimBindProfiles Version: 1.2.0 Depends: R (>= 2.10), methods, Ringo Imports: limma, mclust, Biobase License: GPL-3 MD5sum: 87a55320f5bbac6aa0641fcf209ff67e NeedsCompilation: no Package: simpleaffy Version: 2.40.0 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) MD5sum: 38fed262d3615bb532a50b3f7be664fa NeedsCompilation: yes Package: sizepower Version: 1.34.0 Depends: stats License: LGPL MD5sum: 7c3e1169e057807ad02083d1f91d4ae5 NeedsCompilation: no Package: SJava Version: 0.90.0 Depends: R (>= 2.10.0), methods Imports: methods License: GPL (>= 2) MD5sum: 4d6c692d51bca0728cdcb0697faa0b2a NeedsCompilation: yes Package: SLGI Version: 1.24.0 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 MD5sum: f669f937af67c7d97ef13f0dca2c82d3 NeedsCompilation: no Package: SLqPCR Version: 1.30.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: ae8eb1d37984e10e8cc18377903c2f58 NeedsCompilation: no Package: SMAP Version: 1.28.0 Depends: R (>= 2.10), methods License: GPL-2 MD5sum: 117d4779f6031b58a4c7c707f7055a3d NeedsCompilation: yes Package: SNAGEE Version: 1.4.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: ed62d2d19c147ff2fbdfb13a208c0cc9 NeedsCompilation: no Package: snapCGH Version: 1.34.0 Depends: limma, DNAcopy, methods Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils License: GPL MD5sum: 9b23375405904e772648f346629e368c NeedsCompilation: yes Package: snm Version: 1.12.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: 5401972d8019fd227e340672b2eb805c NeedsCompilation: no Package: SNPchip Version: 2.10.0 Depends: R (>= 2.14.0) Imports: graphics, lattice, grid, foreach, utils, methods, oligoClasses (>= 1.21.12), Biobase, GenomicRanges Suggests: crlmm (>= 1.17.14), IRanges, RUnit Enhances: doSNOW, VanillaICE (>= 1.21.24), RColorBrewer License: LGPL (>= 2) MD5sum: c580d8948e7803c32fe4852599b2d8a3 NeedsCompilation: no Package: snpStats Version: 1.14.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics Suggests: hexbin License: GPL-3 MD5sum: 78a46750b09d13b4b1a56c734b9d3741 NeedsCompilation: yes Package: SomatiCA Version: 1.6.0 Depends: R (>= 2.14.0), lars, DNAcopy, foreach, methods, rebmix, GenomicRanges, IRanges, doParallel Imports: foreach, lars, sn, DNAcopy, methods, rebmix, GenomicRanges, IRanges Enhances: sn, SomatiCAData License: GPL (>= 2) MD5sum: 9eba439906dde84af468685a38015e18 NeedsCompilation: no Package: SomaticSignatures Version: 1.0.1 Depends: R (>= 3.0.2) Imports: GenomeInfoDb, GenomicRanges, IRanges, VariantAnnotation, Biostrings, ggplot2, ggbio, stringr, reshape2, NMF, methods, pcaMethods, gtools Suggests: testthat, knitr, BiocStyle, parallel, BSgenome.Hsapiens.UCSC.hg19, SomaticCancerAlterations, h5vc, h5vcData, fastICA License: GPL-3 MD5sum: 5dafae55c15ab463e91c70cd94f5ab7e NeedsCompilation: no Package: SpacePAC Version: 1.2.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: 70ecf3b63760bf70f1e925b50ddb799a NeedsCompilation: no Package: spade Version: 1.12.2 Depends: R (>= 2.11), igraph, Rclusterpp Imports: Biobase, flowCore Suggests: flowViz License: GPL-2 MD5sum: 29dcc0e64445e44ea25ffa4677a9aad7 NeedsCompilation: yes Package: SpeCond Version: 1.18.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: f6e79eb1bcc5920d5d5ad6810c45a827 NeedsCompilation: no Package: SPEM Version: 1.4.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: e6fb8d80a3fc3182e3af6034337e6667 NeedsCompilation: no Package: SPIA Version: 2.16.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: GPL (>= 2) MD5sum: f4277df77b85734b43e2e968f81f0f87 NeedsCompilation: no Package: spikeLI Version: 2.24.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: 9618f8f0c36917684c484a8636c285ce NeedsCompilation: no Package: spkTools Version: 1.20.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) MD5sum: 9bf3fb6080c5a06c88d412be8a8c00f7 NeedsCompilation: no Package: splicegear Version: 1.36.0 Depends: R (>= 2.6.0), methods, Biobase(>= 2.5.5) Imports: annotate, Biobase, graphics, grDevices, grid, methods, utils, XML License: LGPL MD5sum: f0d8bc46167fa0906172f96a91f1b814 NeedsCompilation: no Package: spliceR Version: 1.6.2 Depends: R (>= 2.15.0), methods, cummeRbund, rtracklayer, VennDiagram, RColorBrewer, plyr Imports: GenomicRanges, IRanges Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome License: GPL (>= 2) MD5sum: 2204a5b10fde1ff44701ce732807d71d NeedsCompilation: yes Package: spliceSites Version: 1.2.0 Depends: methods,rbamtools,refGenome (>= 1.1.2),doBy,Biobase,Biostrings (>= 2.28.0),seqLogo Imports: BiocGenerics License: GPL-2 MD5sum: 4c88ad7d64199233690ccf3f975c2f00 NeedsCompilation: yes Package: SplicingGraphs Version: 1.4.1 Depends: BiocGenerics, IRanges (>= 1.17.43), GenomicRanges (>= 1.15.12), GenomicFeatures, GenomicAlignments (>= 1.0.3), Rgraphviz (>= 2.3.7) Imports: methods, utils, igraph, BiocGenerics, IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments, graph, Rgraphviz Suggests: igraph, Gviz, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: 6fef06690619db1f13c1847da986c84b NeedsCompilation: no Package: splots Version: 1.30.0 Imports: grid, RColorBrewer License: LGPL MD5sum: 836c8e9d2a78bbb43b95acc11c8b1cc0 NeedsCompilation: no Package: spotSegmentation Version: 1.38.0 Depends: R (>= 2.10), mclust License: GPL (>= 2) MD5sum: 732c5054444684acc2d83ecad6c06299 NeedsCompilation: no Package: SQUADD Version: 1.14.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>= 2) MD5sum: 987cde7ac4239a97b0a16eb140a2d5be NeedsCompilation: no Package: SRAdb Version: 1.18.0 Depends: RSQLite (>= 0.8-4) , graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 MD5sum: 25f4ae585b8fcb95d3faf0e07437fb1c NeedsCompilation: no Package: sRAP Version: 1.4.2 Depends: WriteXLS Imports: gplots, pls, ROCR, qvalue License: GPL-3 MD5sum: da87fc6df5ae7e295e466b3664b0a2f2 NeedsCompilation: no Package: sscore Version: 1.36.0 Depends: R (>= 1.8.0), affy, affyio Suggests: affydata License: GPL (>= 2) MD5sum: 6dc0e952ebe683f8802bd84d74a1927d NeedsCompilation: no Package: sSeq Version: 1.2.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) MD5sum: d8f76ad896e9b2aa14a3c8618f262447 NeedsCompilation: no Package: ssize Version: 1.38.0 Depends: gdata, xtable License: LGPL MD5sum: 9b05cd974d7edf7eef28c02b608f2a9f NeedsCompilation: no Package: SSPA Version: 2.4.0 Depends: R (>= 2.12), methods, qvalue, lattice, limma Imports: graphics, stats Suggests: BiocStyle, genefilter, edgeR, DESeq License: GPL (>= 2) MD5sum: 8253a9b489e650e35915ce50f9d403fb NeedsCompilation: yes Package: staRank Version: 1.6.0 Depends: methods, cellHTS2, R (>= 2.10) License: GPL MD5sum: aa0ac20e85793eb0fa937a0648b5a304 NeedsCompilation: no Package: Starr Version: 1.20.0 Depends: Ringo, affy, affxparser Imports: pspline, MASS, zlibbioc License: Artistic-2.0 MD5sum: 04a8f87bfe3472d8d6e18c2f7f67d9ec NeedsCompilation: yes Package: stepNorm Version: 1.36.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL MD5sum: 38485d4e8ecd0c4d3411eb4c013560b4 NeedsCompilation: no Package: stepwiseCM Version: 1.10.0 Depends: R (>= 2.14), randomForest, MAclinical, tspair, pamr, snowfall, glmpath, penalized, e1071, Biobase License: GPL (> 2) MD5sum: ebe854cf34af3b07a1e42885cf518e78 NeedsCompilation: no Package: Streamer Version: 1.10.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 MD5sum: 66de8a98c8e8c47f57e9067832790b01 NeedsCompilation: yes Package: STRINGdb Version: 1.3.2 Depends: R (>= 2.14.0), png, sqldf, plyr, igraph, RCurl, plotrix, methods Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: dfad3e5fdd47f370501a54c9d08da139 NeedsCompilation: no Package: supraHex Version: 1.2.0 Depends: R (>= 3.0.2), hexbin Imports: ape, MASS License: GPL-2 MD5sum: f8b848d2374190d367bc502eedc6a9ba NeedsCompilation: no Package: survcomp Version: 1.14.0 Depends: R (>= 2.10), survival, prodlim Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta Suggests: Hmisc, CPE, clinfun, survJamda, Biobase, xtable License: Artistic-2.0 MD5sum: dc816580fb2c8adc3c51a981c5ea8913 NeedsCompilation: yes Package: Sushi Version: 1.0.0 Depends: R (>= 2.10), zoo,biomaRt Imports: graphics, grDevices License: GPL (>= 2) MD5sum: 7e83e9be9a7b84a4ed5ffa3fa2a09cf1 NeedsCompilation: no Package: sva Version: 3.10.0 Depends: R (>= 2.8), corpcor, mgcv Imports: graphics, stats Suggests: limma,pamr,bladderbatch License: Artistic-2.0 MD5sum: 11bf3e771369fc49964e20df9bf3961a NeedsCompilation: yes Package: SwimR Version: 1.2.0 Depends: R (>= 3.0.0), methods, gplots (>= 2.10.1), heatmap.plus (>= 1.3), signal (>= 0.7), R2HTML (>= 2.2.1) Imports: methods License: LGPL-2 MD5sum: 6b5d9ddc0e607f5ea7f491d4b3ee9c88 NeedsCompilation: no Package: synapter Version: 1.6.0 Depends: R (>= 2.15), methods, MSnbase Imports: hwriter, tcltk, tcltk2, RColorBrewer, lattice, qvalue, multtest, utils, Biobase, knitr, Biostrings, cleaver, BiocParallel Suggests: synapterdata, xtable License: GPL-2 MD5sum: 4a81ce20ceb066d7215b9146e909005b NeedsCompilation: no Package: TargetScore Version: 1.2.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: abaf217cb7043376dfb451a522344689 NeedsCompilation: no Package: TargetSearch Version: 1.20.0 Depends: R (>= 2.7.0), mzR Imports: graphics, grDevices, methods, stats, tcltk, utils Suggests: TargetSearchData License: GPL (>= 2) MD5sum: 2236d72c8fe72ca19724709f0dc408de NeedsCompilation: yes Package: TCC Version: 1.4.0 Depends: R (>= 2.15), methods, DESeq, DESeq2, edgeR, baySeq, ROC Imports: samr Suggests: RUnit, BiocGenerics Enhances: snow License: GPL-2 MD5sum: f55cfdfc3efdb088f35fd0899834c897 NeedsCompilation: no Package: TDARACNE Version: 1.14.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 MD5sum: 673f6fc29eb54f9a04610244844aa307 NeedsCompilation: no Package: TEQC Version: 3.4.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: f1385a0a3d41d9f2e88f57d8647efbd0 NeedsCompilation: no Package: ternarynet Version: 1.8.0 Depends: R (>= 2.10.0), methods Imports: utils, igraph License: GPL (>= 2) MD5sum: 90da0c88dd2fa9bca9d6c02897e5e04e NeedsCompilation: yes Package: TFBSTools Version: 1.2.0 Depends: R (>= 3.0.1) Imports: Biostrings(>= 2.29.19), RSQLite(>= 0.11.4), seqLogo, GenomicRanges(>= 1.13.50), caTools(>= 1.14), XVector(>= 0.2.0), rtracklayer(>= 1.22.0), BSgenome(>= 1.30.0), IRanges(>= 1.19.38), methods, gtools(>= 3.0.0), CNEr(>= 0.99.8), BiocParallel(>= 0.5.6), DirichletMultinomial(>= 1.5.1) Suggests: JASPAR2014(>= 0.99.3), RUnit, BiocGenerics License: GPL-2 MD5sum: 71c5d3ded26380665a9aeb98f93ee452 NeedsCompilation: yes Package: tigre Version: 1.18.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, lumi License: AGPL-3 MD5sum: e274751a465dbacb3a008a92e7c8cd90 NeedsCompilation: yes Package: tilingArray Version: 1.42.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: 81a5cfcc3e88857ddd8fd397176f9447 NeedsCompilation: yes Package: timecourse Version: 1.36.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 411753756e56d054647dbb6e8d4cb36d NeedsCompilation: no Package: TitanCNA Version: 1.0.0 Depends: R (>= 3.0.1), foreach (>= 1.4.0), HMMcopy (>= 1.2.0) License: file LICENSE MD5sum: aac773f2dc265302601c485ca1f5db99 NeedsCompilation: yes Package: tkWidgets Version: 1.42.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: 291747843fa5466ae8f4e635b907f40f NeedsCompilation: no Package: topGO Version: 2.16.0 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 MD5sum: 6cbf5c7d02f32cc48ffe18e542a1644c NeedsCompilation: no Package: trackViewer Version: 1.0.2 Depends: R (>= 3.1.0), methods, GenomicRanges, grid, gWidgetstcltk Imports: GenomicAlignments, GenomicFeatures, Gviz, pbapply, Rsamtools, rtracklayer, scales Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: cad96a9ff1f7ddd9bd8357c8454f56f9 NeedsCompilation: no Package: tRanslatome Version: 1.2.0 Depends: R (>= 2.15.0), methods, limma, sigPathway, samr, anota, DESeq, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix License: LGPL MD5sum: f6c19f53c260c6b0ed5f7303cac37548 NeedsCompilation: no Package: TransView Version: 1.8.0 Depends: methods,GenomicRanges Imports: Rsamtools,zlibbioc,gplots,IRanges LinkingTo: Rsamtools Suggests: RUnit,pasillaBamSubset License: GPL-3 MD5sum: 9249064e50d53e846f6618850c32cec3 NeedsCompilation: yes Package: triform Version: 1.6.0 Depends: R (>= 2.11.0), IRanges, yaml Imports: IRanges, yaml, BiocGenerics Suggests: RUnit License: GPL-2 MD5sum: c1f1e3ee56a73d3407ff4a80f48a0cfe NeedsCompilation: no Package: trigger Version: 1.10.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: 907154436e8ba6badeae7bc712d12d38 NeedsCompilation: yes Package: trio Version: 3.2.1 Depends: R (>= 3.0.1) Suggests: survival, haplo.stats, mcbiopi, siggenes, splines, LogicReg (>= 1.5.3), logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: 640120d20d4b596e2279ac5cd628d188 NeedsCompilation: no Package: triplex Version: 1.4.0 Depends: R (>= 2.15.0), IRanges (>= 1.21.10), XVector (>= 0.3.2), Biostrings (>= 2.31.3) Imports: methods, grid, GenomicRanges LinkingTo: IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs License: BSD_2_clause + file LICENSE MD5sum: 1e922e463a2fc4f7db7f41d55d66dff8 NeedsCompilation: yes Package: tspair Version: 1.22.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 MD5sum: 8a231a0133fc6181702bf628e74065c9 NeedsCompilation: yes Package: TSSi Version: 1.10.0 Depends: R (>= 2.13.2), BiocGenerics (>= 0.3.2) Imports: BiocGenerics, methods, Hmisc, minqa, stats, Biobase (>= 0.3.2), plyr, IRanges Suggests: rtracklayer Enhances: parallel License: GPL-3 MD5sum: 3e63b4ab888959e90b33a255a139f144 NeedsCompilation: yes Package: TurboNorm Version: 1.12.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata License: LGPL MD5sum: e7ca4df119b0fe1e58dc8d88704ad5f4 NeedsCompilation: yes Package: tweeDEseq Version: 1.10.0 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 167f06313dd9325c74f8b030a8d31f61 NeedsCompilation: yes Package: twilight Version: 1.40.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: 8a8dae8f845b838d75a5a1f11a22defa NeedsCompilation: yes Package: TypeInfo Version: 1.30.0 Depends: methods Suggests: Biobase License: BSD MD5sum: 04ee5ce02eb092bda9b03566db050298 NeedsCompilation: no Package: UNDO Version: 1.0.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: f9977e9938d1b77c2b19f3370101cd91 NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.0.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: 8e8382a834d1d282a4c8555e2de8cf35 NeedsCompilation: no Package: UniProt.ws Version: 2.4.2 Depends: RSQLite, RCurl, methods, utils Imports: BiocGenerics, AnnotationDbi Suggests: RUnit License: Artistic License 2.0 MD5sum: 54757295b744d6801727af254f7e7d9a NeedsCompilation: no Package: VanillaICE Version: 1.26.1 Depends: R (>= 3.0.0) Imports: stats, utils, methods, Biobase, oligoClasses (>= 1.21.12),lattice, IRanges (>= 1.13.22), grid, msm, iterators, foreach, GenomicRanges, matrixStats Suggests: genomewidesnp6Crlmm (>= 1.0.7), hapmapsnp6, RColorBrewer, genefilter, RSQLite, foreach, RUnit, pd.mapping50k.hind240, SNPchip (>= 2.5.7), doSNOW Enhances: DNAcopy, crlmm (>= 1.17.14) License: LGPL-2 MD5sum: 643fab25e414cbda9e58217cefe4426f NeedsCompilation: yes Package: VariantAnnotation Version: 1.10.5 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.7.7), GenomicRanges (>= 1.13.51), Rsamtools (>= 1.15.5) Imports: IRanges (>= 1.21.43), XVector, Biostrings (>= 2.31.19), Biobase, AnnotationDbi (>= 1.17.11), zlibbioc, BSgenome, GenomicFeatures (>= 1.15.15), DBI, utils, rtracklayer LinkingTo: IRanges, XVector, Biostrings, Rsamtools Suggests: RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle License: Artistic-2.0 MD5sum: 96c8dea7917fd57839fec31f54963f30 NeedsCompilation: yes Package: VariantFiltering Version: 1.0.4 Depends: R (>= 3.0.0), methods, BiocGenerics (>= 0.9.1) Imports: DBI, RSQLite (>= 0.8-1), Biobase, IRanges (>= 1.21.13), AnnotationDbi, BiocParallel, Biostrings (>= 2.29.19), GenomicRanges, Rsamtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, VariantAnnotation, shiny LinkingTo: IRanges, XVector, Biostrings Suggests: BiocStyle, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20120608, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 85b0ff8dd34ced359a999987a53dc076 NeedsCompilation: yes Package: VariantTools Version: 1.6.1 Depends: IRanges (>= 1.19.34), GenomicRanges (>= 1.13.43), VariantAnnotation (>= 1.7.35), methods Imports: Rsamtools (>= 1.11.10), BiocGenerics, Biostrings, parallel, gmapR (>= 1.5.15), GenomicFeatures, Matrix, rtracklayer, BiocParallel, GenomeInfoDb Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph License: Artistic-2.0 MD5sum: eaa3c14f0a7e65691461a4b35a95d6b1 NeedsCompilation: no Package: vbmp Version: 1.32.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 5844b6aa7d281647fa8b12fa16ca255b NeedsCompilation: no Package: Vega Version: 1.12.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: d75fd44d9eeb08a30dc95636a878036e NeedsCompilation: yes Package: VegaMC Version: 3.2.0 Depends: R (>= 2.10.0), biomaRt, Biobase, genoset Imports: methods License: GPL-2 MD5sum: e0e608a20025630a9abf71eda868f81a NeedsCompilation: yes Package: viper Version: 1.0.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats Suggests: bcellViper License: GPL (>= 2) MD5sum: d1b0013e02df96da1bf6845e51d713b3 NeedsCompilation: no Package: virtualArray Version: 1.8.0 Depends: R (>= 2.15.0), BiocGenerics, methods, plyr, preprocessCore Imports: affy, affyPLM, AnnotationDbi, Biobase, gcrma, GEOquery, graphics, methods, reshape2, stats, utils, tseries, outliers Suggests: affydata, plier, limma, lumi, org.Hs.eg.db Enhances: multicore,BiocParallel License: GPL-3 MD5sum: 177f2e4928c77243e254e3d29cd7292e NeedsCompilation: no Package: vsn Version: 3.32.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: methods, affy (>= 1.23.4), limma, lattice Suggests: affydata, hgu95av2cdf License: Artistic-2.0 MD5sum: 616aa7372e5ec6cce50127919689cf68 NeedsCompilation: yes Package: vtpnet Version: 0.4.1 Depends: R (>= 3.0.0), graph, GenomicRanges Suggests: MotifDb, VariantAnnotation, Rgraphviz, gwascat License: Artistic-2.0 MD5sum: 03bfc87cfb84f8863e6632339c0cb348 NeedsCompilation: no Package: wateRmelon Version: 1.4.0 Depends: R (>= 2.10), limma, methods, matrixStats, methylumi, lumi, IlluminaHumanMethylation450k.db, ROC Suggests: RPMM Enhances: minfi, methylumi, IMA License: GPL-3 MD5sum: 0eb6266592fec7512a05ad8b4c9cbc3b NeedsCompilation: no Package: waveTiling Version: 1.6.0 Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, IRanges Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart12 License: GPL (>= 2) MD5sum: a037c8b10d8310a87eb13b795a5c4e46 NeedsCompilation: yes Package: weaver Version: 1.30.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 32bd56e8162a7b1b15aa9c59a6ea0d30 NeedsCompilation: no Package: webbioc Version: 1.36.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocInstaller License: GPL (>= 2) MD5sum: f0be6ec646756ee44fd2987c1c7f18b4 NeedsCompilation: no Package: widgetTools Version: 1.42.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: a51dbb312d23917767fad4829c47fc5a NeedsCompilation: no Package: xcms Version: 1.40.0 Depends: R (>= 2.14.0), methods, mzR (>= 1.1.6), BiocGenerics, Biobase Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>= 1.5.2), RANN, RUnit Enhances: Rgraphviz, Rmpi, XML License: GPL (>= 2) + file LICENSE MD5sum: 24eefb97a2059dc89835dd595f45017f NeedsCompilation: yes Package: XDE Version: 2.10.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), methods, graphics Imports: Biobase, BiocGenerics, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils, mvtnorm Suggests: siggenes, genefilter, MASS, RColorBrewer, GeneMeta, RUnit Enhances: coda License: LGPL-2 MD5sum: c9481e679300257aeff6f9ae24499dd2 NeedsCompilation: yes Package: xmapbridge Version: 1.22.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: d8399dc21608e9e6c05eb3cc3d215336 NeedsCompilation: no Package: xps Version: 1.24.1 Depends: R (>= 2.6.0), methods, utils Suggests: tools License: GPL (>= 2.0) MD5sum: de7bb04d94476ebd7b0608cfadfecc70 NeedsCompilation: yes Package: XVector Version: 0.4.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.7.2), IRanges (>= 1.21.25) Imports: methods, BiocGenerics, IRanges LinkingTo: IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: 4fa3e58a5251357478b4282d1d08e3e5 NeedsCompilation: yes Package: yaqcaffy Version: 1.24.0 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 MD5sum: aaa84506702f94f98b620b8602225fb7 NeedsCompilation: no Package: zlibbioc Version: 1.10.0 License: Artistic-2.0 + file LICENSE MD5sum: 88e9c6b8aa87ab12c8d01932e447aa2f NeedsCompilation: yes