Functions that are needed by many other packages or which replace R functions.
Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon
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| biocViews |
Infrastructure, Software |
| Version |
2.36.2 |
| In Bioconductor since |
BioC 1.6 (R-2.1) or earlier (> 12.5 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 2.10), BiocGenerics(>= 0.3.2), utils |
| Imports |
methods |
| LinkingTo |
|
| Suggests |
tools, tkWidgets, ALL, RUnit, golubEsets |
| SystemRequirements |
|
| Enhances |
|
| URL |
|
| Depends On Me |
a4Base, a4Core, ACME, affy, affycomp, affycompData, affyContam, affycoretools, affyPLM, affyQCReport, AGDEX, AgiMicroRna, AIMS, ALL, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, antiProfilesData, ArrayExpress, arrayMvout, ArrayTools, BAGS, bcellViper, beadarray, beadarrayExampleData, beadarraySNP, bgx, BicARE, bigmelon, BiocCaseStudies, bioDist, BioMVCClass, BioQC, birta, bladderbatch, BLMA, BrainStars, CAMERA, cancerclass, cancerdata, Cardinal, casper, Category, categoryCompare, CCl4, CCPROMISE, cellHTS2, ceu1kg, ceuhm3, CGHbase, CGHcall, CGHregions, charm, cheung2010, chimera, chroGPS, ClassifyR, clippda, CLL, clusterStab, CMA, cn.farms, codelink, colonCA, convert, copa, covEB, covRNA, CRCL18, curatedBreastData, curatedMetagenomicData, davidTiling, DESeq, DEXSeq, DFP, diggit, diggitdata, DLBCL, doppelgangR, dressCheck, dsQTL, DSS, dualKS, dyebias, EBarrays, EDASeq, edge, EGSEA, eisa, EnrichmentBrowser, epigenomix, epivizrData, etec16s, ExiMiR, ExpressionAtlas, fabia, fabiaData, factDesign, fastseg, fibroEset, flowBeads, frma, gaga, gaschYHS, gCMAPWeb, GeneAnswers, GeneExpressionSignature, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, GeneSelector, geNetClassifier, GEOquery, GGdata, GOexpress, GOFunction, golubEsets, goProfiles, GOstats, GRridge, GSE62944, GSEABase, GSEAlm, GSVAdata, GWASTools, hapFabia, harbChIP, HCsnip, HELP, Hiiragi2013, hmyriB36, hopach, HTqPCR, htSeqTools, HumanAffyData, humanStemCell, HybridMTest, iBMQ, iCheck, IdeoViz, idiogram, InPAS, INSPEcT, isobar, iterativeBMA, IVAS, Iyer517, kidpack, leeBamViews, leukemiasEset, LMGene, lumi, lumiBarnes, lungExpression, macat, mAPKL, MAQCsubset, MAQCsubsetAFX, MAQCsubsetILM, maSigPro, massiR, MEAL, MergeMaid, metabomxtr, metagenomeFeatures, metagenomeSeq, metavizr, MethPed, methyAnalysis, methylumi, Mfuzz, MiChip, mimager, MIMOSA, MineICA, MiRaGE, miRcomp, miRNATarget, MLInterfaces, MLSeq, MMDiff2, MmPalateMiRNA, monocle, msd16s, MSnbase, Mulcom, MultiDataSet, multtest, mvoutData, NanoStringDiff, Neve2006, NOISeq, nondetects, normalize450K, NormqPCR, oligo, oneChannelGUI, OrderedList, OTUbase, OutlierD, PADOG, pandaR, PAnnBuilder, panp, pcaMethods, pcot2, pdInfoBuilder, pdmclass, pepStat, PGSEA, phenoTest, PLPE, plrs, prada, PREDA, PREDAsampledata, ProData, pRolocGUI, PROMISE, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, prot2D, pumadata, qpcrNorm, R453Plus1Toolbox, RbcBook1, rbsurv, rcellminer, rcellminerData, ReadqPCR, reb, RefPlus, rHVDM, Ringo, Risa, Rmagpie, rMAT, RNAinteract, rnaSeqMap, Rnits, Roleswitch, RpsiXML, RTCA, RTopper, RUVnormalizeData, RUVSeq, safe, SCAN.UPC, scater, SeqGSEA, sigaR, SigCheck, siggenes, simpleaffy, simulatorZ, SpeCond, SPEM, SpikeInSubset, spkTools, splicegear, spliceSites, splineTimeR, stepwiseCM, STROMA4, SummarizedExperiment, TCGAcrcmiRNA, TCGAcrcmRNA, TDARACNE, tigre, tilingArray, topGO, tRanslatome, tspair, tweeDEseqCountData, twilight, UNDO, variancePartition, VegaMC, viper, vsn, wateRmelon, waveTiling, webbioc, xcms, XDE, yarn, yeastCC |
| Imports Me |
ABarray, aCGH, adSplit, affyILM, affyQCReport, AgiMicroRna, AnalysisPageServer, annmap, annotate, AnnotationDbi, AnnotationHubData, annotationTools, ArrayExpressHTS, arrayQualityMetrics, ArrayTools, attract, ballgown, BayesKnockdown, BgeeDB, biobroom, bioCancer, biocViews, BioNet, BioSeqClass, biosigner, biosvd, birte, BiSeq, blima, BrainStars, bsseq, BubbleTree, CAFE, canceR, ccTutorial, ceu1kgv, cgdv17, CGHnormaliter, charm, ChIPpeakAnno, ChIPQC, ChIPXpress, ChromHeatMap, clipper, cn.mops, cogena, ConsensusClusterPlus, crlmm, crossmeta, cummeRbund, cycle, cydar, cytofkit, CytoML, ddCt, DESeq2, DeSousa2013, destiny, diffloop, discordant, DOQTL, easyRNASeq, EBarrays, ecolitk, EGAD, ensembldb, erma, esetVis, ExiMiR, farms, ffpe, FindMyFriends, Fletcher2013a, flowClust, flowCore, flowFP, flowMatch, flowMeans, flowStats, flowType, flowUtils, flowViz, flowWorkspace, FourCSeq, frma, frmaTools, FunciSNP, gCMAP, gCrisprTools, gcrma, genbankr, geneClassifiers, genefilter, GeneMeta, geneRecommender, GeneRegionScan, GeneSelectMMD, GENESIS, GenomicFeatures, GenomicInteractions, GEOsubmission, gespeR, GGBase, ggbio, GGtools, girafe, GISPA, Glimma, globaltest, gmapR, GOFunction, GoogleGenomics, GOstats, gQTLstats, GSRI, GSVA, Gviz, Harshlight, HEM, HTqPCR, HTSFilter, IdMappingAnalysis, IHWpaper, imageHTS, ImmuneSpaceR, ImpulseDE2, IsoGeneGUI, JunctionSeq, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, kimod, lapmix, LINC, LiquidAssociation, LVSmiRNA, maanova, makecdfenv, maSigPro, MAST, mBPCR, MCRestimate, MeSHDbi, metaArray, methyAnalysis, MethylAid, methylumi, MiChip, MIGSA, minfi, MinimumDistance, MiPP, mmnet, MmPalateMiRNA, mogsa, MoonlightR, MoPS, MSnID, MultiAssayExperiment, multiscan, mzR, NanoStringQCPro, ncdfFlow, npGSEA, nucleR, OGSA, oligoClasses, openCyto, oposSOM, oppar, OrderedList, OrganismDbi, PAnnBuilder, panp, Pbase, pbcmc, PCpheno, PharmacoGx, phyloseq, piano, plateCore, plethy, plgem, plier, podkat, POST, ppiStats, prada, prebs, proFIA, pRoloc, pRolocdata, PROMISE, ProteomicsAnnotationHubData, PSEA, psygenet2r, puma, pvac, pvca, pwOmics, qcmetrics, QDNAseq, qpgraph, QUALIFIER, quantro, QuasR, qusage, randPack, readat, ReadqPCR, ReportingTools, RforProteomics, RGalaxy, RIVER, Rmagpie, RMassBank, rMAT, rols, ropls, ROTS, rqubic, Rtreemix, RUVnormalize, SAGx, scran, SeqVarTools, ShortRead, sigsquared, SimBindProfiles, simpleaffy, SLGI, SMITE, SNPchip, SomaticSignatures, spkTools, splatter, splicegear, STATegRa, subSeq, switchde, synapter, TEQC, TFBSTools, timecourse, ToPASeq, TPP, TSSi, twilight, uSORT, VanillaICE, VariantAnnotation, VariantFiltering, VariantTools, wateRmelon, XBSeq, XDE, yri1kgv |
| Suggests Me |
BiocCaseStudies, BiocCheck, BiocGenerics, biotmleData, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, BSgenome, ccTutorial, CellMapper, cellTree, clustComp, coseq, CountClust, DAPAR, DART, dyebiasexamples, epivizr, epivizrStandalone, farms, genefu, GenomicRanges, GlobalAncova, GSAR, Heatplus, interactiveDisplay, kebabs, les, limma, Logolas, mammaPrintData, mAPKLData, messina, msa, multiClust, nem, OSAT, pkgDepTools, rheumaticConditionWOLLBOLD, ROC, RTCGA, SeqArray, seventyGeneData, survcomp, TargetScore, TCGAbiolinks, tkWidgets, TypeInfo, vbmp, widgetTools, yeastExpData, yeastRNASeq |
| Build Report |
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