Biobase

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Biobase.

Biobase: Base functions for Bioconductor


Bioconductor version: 3.9

Functions that are needed by many other packages or which replace R functions.

Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("Biobase")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biobase")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Biobase")
An introduction to Biobase and ExpressionSets PDF R Script
esApply Introduction PDF R Script
Notes for eSet developers PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Infrastructure, Software
Version 2.44.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License Artistic-2.0
Depends R (>= 2.10), BiocGenerics(>= 0.27.1), utils
Imports methods
System Requirements
URL
See More
Suggests tools, tkWidgets, ALL, RUnit, golubEsets
Linking To
Enhances
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, biosigner, birta, bladderbatch, BLMA, BrainStars, brgedata, CAMERA, cancerclass, cancerdata, casper, Category, categoryCompare, CCl4, CCPROMISE, cellHTS2, ceu1kg, ceuhm3, CGHbase, CGHcall, CGHregions, charm, chimera, chroGPS, 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, epigenomix, epivizrData, etec16s, EuPathDB, ExiMiR, ExpressionAtlas, fabia, fabiaData, factDesign, fastseg, fibroEset, flowBeads, frma, gaga, gaschYHS, gCMAPWeb, GeneAnswers, GeneExpressionSignature, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, geNetClassifier, GEOquery, GGdata, GOexpress, GOFunction, golubEsets, goProfiles, GOstats, GSE62944, GSEABase, GSEABenchmarkeR, GSEAlm, GSVAdata, GWASTools, hapFabia, harbChIP, 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, maEndToEnd, mAPKL, MAQCsubset, MAQCsubsetAFX, MAQCsubsetILM, massiR, MEAL, MergeMaid, metabomxtr, metagenomeFeatures, metagenomeSeq, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, metavizr, MethPed, methyAnalysis, methylumi, Mfuzz, MiChip, mimager, MIMOSA, MineICA, MiRaGE, miRcomp, miRNATarget, MLInterfaces, MMDiff2, MmPalateMiRNA, monocle, msd16s, MSnbase, Mulcom, MultiDataSet, multtest, mvoutData, NanoStringDiff, Neve2006, NOISeq, nondetects, normalize450K, NormqPCR, oligo, omicRexposome, OrderedList, OTUbase, OutlierD, PADOG, pandaR, panp, pcaMethods, pcot2, pdInfoBuilder, pepStat, PGSEA, phenoTest, PLPE, plrs, prada, PREDA, PREDAsampledata, ProData, pRolocGUI, PROMISE, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, pumadata, qpcrNorm, qPLEXanalyzer, R453Plus1Toolbox, RbcBook1, rbsurv, rcellminer, rcellminerData, ReadqPCR, reb, RefPlus, rexposome, rHVDM, Ringo, Risa, Rmagpie, rMAT, RNAinteract, rnaSeqMap, Rnits, Roleswitch, ropls, RpsiXML, RTCA, RTopper, RUVnormalizeData, RUVSeq, safe, SCAN.UPC, SeqGSEA, sigaR, SigCheck, siggenes, simpleaffy, simulatorZ, singleCellTK, SpeCond, SPEM, SpikeInSubset, spkTools, splicegear, spliceSites, splineTimeR, STROMA4, SummarizedExperiment, TCGAcrcmiRNA, TCGAcrcmRNA, TDARACNE, tigre, tilingArray, topGO, TPP, tRanslatome, tspair, tweeDEseqCountData, twilight, UNDO, variancePartition, VegaMC, viper, vsn, wateRmelon, waveTiling, webbioc, xcms, XDE, XINA, yarn, yeastCC
Imports Me ABarray, ACE, aCGH, adSplit, affyILM, affyQCReport, AgiMicroRna, AnalysisPageServer, ANF, annmap, annotate, AnnotationHubData, annotationTools, ArrayExpressHTS, arrayQualityMetrics, ArrayTools, attract, ballgown, BASiCS, BayesKnockdown, BgeeDB, biobroom, bioCancer, biocViews, BioNet, BioSeqClass, biosvd, birte, BiSeq, blima, BloodCancerMultiOmics2017, BrainStars, bsseq, BubbleTree, CAFE, CAMTHC, canceR, Cardinal, CATALYST, ccTutorial, CellScore, CellTrails, ceu1kgv, cgdv17, CGHnormaliter, charm, ChIPpeakAnno, ChIPQC, ChIPXpress, ChromHeatMap, chromswitch, cicero, clipper, CluMSID, cn.mops, COCOA, coexnet, cogena, ConsensusClusterPlus, consensusDE, consensusOV, coRdon, crlmm, crossmeta, cummeRbund, cycle, cydar, CytoML, ddCt, deco, DEGreport, DESeq2, DeSousa2013, destiny, diffloop, discordant, DOQTL, easyRNASeq, EBarrays, ecolitk, EGAD, ENmix, ensembldb, erma, esetVis, ExiMiR, ExpressionNormalizationWorkflow, farms, ffpe, FindMyFriends, Fletcher2013a, flowClust, flowCore, flowFP, flowMatch, flowMeans, flowStats, flowType, flowUtils, flowViz, flowWorkspace, FourCSeq, frma, frmaTools, FunciSNP, GAPGOM, gCMAP, gCrisprTools, gcrma, genbankr, geneClassifiers, genefilter, GeneMeta, geneRecommender, GeneRegionScan, GeneSelectMMD, GENESIS, GenomicFeatures, GenomicInteractions, GenomicScores, GEOsubmission, gep2pep, gespeR, GGBase, ggbio, GGtools, girafe, GISPA, GlobalAncova, globaltest, gmapR, GOFunction, gQTLstats, GSRI, GSVA, Gviz, Harshlight, HEM, hgu133plus2CellScore, HTqPCR, HTSFilter, IdMappingAnalysis, IHWpaper, imageHTS, ImmuneSpaceR, ImpulseDE2, InTAD, IsoGeneGUI, isomiRs, iterClust, JunctionSeq, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, kimod, kissDE, lapmix, LINC, LiquidAssociation, LRBaseDbi, LVSmiRNA, maanova, makecdfenv, maSigPro, MAST, mBPCR, MCRestimate, mcsurvdata, MeSHDbi, metaArray, methyAnalysis, MethylAid, methylumi, mfa, MiChip, MIGSA, minfi, MinimumDistance, MiPP, MIRA, miRSM, MLSeq, MmPalateMiRNA, MOFA, mogsa, MoonlightR, MoPS, MSnID, MTseeker, MultiAssayExperiment, multiscan, mzR, NanoStringQCPro, ncdfFlow, NormalyzerDE, npGSEA, nucleR, OGSA, oligoClasses, ontoProc, openCyto, oposSOM, oppar, OrderedList, OrganismDbi, OUTRIDER, panp, PathwaySplice, Pbase, PCpheno, phantasus, PharmacoGx, phemd, phyloseq, piano, plateCore, plethy, plgem, plier, podkat, POST, PowerExplorer, ppiStats, prada, prebs, PrInCE, proBatch, proFIA, progeny, pRoloc, pRolocdata, PROMISE, PROPS, ProteomicsAnnotationHubData, PSEA, psygenet2r, puma, pvac, pvca, pwOmics, qcmetrics, QDNAseq, qpgraph, QUALIFIER, quantro, QuasR, qusage, randPack, readat, ReportingTools, restfulSE, RGalaxy, RIVER, Rmagpie, RMassBank, rMAT, rols, ROTS, rqubic, rScudo, Rtreemix, RUVnormalize, SAGx, scmap, seqc, SeqVarTools, ShortRead, sigsquared, SimBindProfiles, simpleaffy, singscore, SLGI, SMITE, SNPchip, SomaticSignatures, spkTools, splicegear, SPONGE, STATegRa, subSeq, synapter, TEQC, TFBSTools, timecourse, TMixClust, TnT, ToPASeq, topdownr, TSSi, TTMap, twilight, uSORT, VanillaICE, VariantAnnotation, VariantFiltering, VariantTools, vidger, vulcan, wateRmelon, XBSeq, Xeva, yri1kgv
Suggests Me AUCell, BiocCaseStudies, BiocCheck, BiocGenerics, BiocOncoTK, biotmleData, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, BSgenome, ccTutorial, CellMapper, cellTree, clustComp, coseq, CountClust, DAPAR, DART, dcanr, dyebiasexamples, EpiDISH, epivizr, epivizrChart, epivizrStandalone, farms, genefu, GENIE3, GenomicRanges, GSAR, Heatplus, HMP16SData, interactiveDisplay, kebabs, les, limma, Logolas, M3Drop, mammaPrintData, mAPKLData, mCSEA, messina, methyvimData, msa, multiClust, nem, OSAT, PCAtools, pkgDepTools, RcisTarget, RegParallel, rheumaticConditionWOLLBOLD, ROC, RTCGA, scater, scmeth, scran, SeqArray, seventyGeneData, slinky, stageR, survcomp, TargetScore, TCGAbiolinks, TFutils, TimeSeriesExperiment, tkWidgets, TypeInfo, vbmp, widgetTools, yeastExpData, yeastRNASeq
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Biobase_2.44.0.tar.gz
Windows Binary Biobase_2.44.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) Biobase_2.44.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Biobase
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Biobase
Bioc Package Browser https://code.bioconductor.org/browse/Biobase/
Package Short Url https://bioconductor.org/packages/Biobase/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive