Biobase

This is the released version of Biobase; for the devel version, see Biobase.

Biobase: Base functions for Bioconductor

Bioconductor version: Release (3.23)

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

Author: R. Gentleman [aut], V. Carey [aut], M. Morgan [aut], S. Falcon [aut], Haleema Khan [ctb] ('esApply' and 'BiobaseDevelopment' vignette translation from Sweave to Rmarkdown / HTML), Bioconductor Package Maintainer [cre]

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

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") 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	HTML	R Script
Notes for eSet developers	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, Software
Version	2.72.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21 years)
License	Artistic-2.0
Depends	R (>= 2.10), BiocGenerics(>= 0.27.1), utils
Imports	methods
System Requirements
URL	https://bioconductor.org/packages/Biobase
Bug Reports	https://github.com/Bioconductor/Biobase/issues

Suggests	tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma
Linking To
Enhances
Depends On Me	ACME, affy, affycomp, affyContam, affycoretools, affyPLM, AGDEX, AIMS, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, ArrayExpress, arrayMvout, BAGS, bandle, beadarray, BicARE, bigmelon, BioMVCClass, BioQC, BLMA, borealis, CAMERA, cancerclass, casper, Category, categoryCompare, CCPROMISE, CGHbase, CGHcall, CGHregions, clippda, clusterStab, CMA, cn.farms, codelink, convert, copa, covEB, covRNA, CytoMDS, DEXSeq, DFP, diggit, doppelgangR, DSS, dyebias, EBarrays, EDASeq, edge, EGSEA, epigenomix, epivizrData, ExiMiR, ExpressionAtlas, fabia, factDesign, fastseg, flowBeads, frma, gaga, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, geNetClassifier, GeoDiff, GeomxTools, GEOquery, GOexpress, goProfiles, GOstats, GSEABase, GSEABenchmarkeR, GSEAlm, GWASTools, hapFabia, HELP, hopach, HTqPCR, HybridMTest, iCheck, IdeoViz, idiogram, INSPEcT, isobar, iterativeBMA, IVAS, lumi, made4, massiR, MEAL, metagenomeSeq, MethPed, methylumi, Mfuzz, MiChip, microbiomeExplorer, mimager, MiRaGE, miRcomp, MLInterfaces, MMDiff2, monocle, MSnbase, Mulcom, MultiDataSet, multtest, NanoStringDiff, NanoStringNCTools, NanoTube, NOISeq, nondetects, normalize450K, NormqPCR, octad, oligo, omicRexposome, OrderedList, OTUbase, pandaR, panp, pcaMethods, pdInfoBuilder, pepStat, phenoTest, PLPE, POWSC, PREDA, pRolocGUI, PROMISE, qpcrNorm, qPLEXanalyzer, R453Plus1Toolbox, RbcBook1, rbsurv, rcellminer, ReadqPCR, rexposome, Rmagpie, Rnits, RTopper, RUVSeq, safe, SCAN.UPC, SeqGSEA, SigCheck, siggenes, singleCellTK, SpeCond, SPEM, spkTools, splineTimeR, SummarizedExperiment, tigre, tilingArray, topGO, TPP, tRanslatome, UNDO, VegaMC, viper, vsn, wateRmelon, webbioc, XDE, yarn, EuPathDB, affycompData, ALL, bcellViper, beadarrayExampleData, bladderbatch, brgedata, cancerdata, CCl4, CLL, colonCA, CRCL18, curatedBreastData, curatedCRCData, curatedOvarianData, davidTiling, diggitdata, DLBCL, dressCheck, etec16s, fabiaData, fibroEset, gaschYHS, golubEsets, GSE103322, GSE13015, GSE62944, GSVAdata, harbChIP, Hiiragi2013, HumanAffyData, humanStemCell, Iyer517, kidpack, leeBamViews, leukemiasEset, lumiBarnes, lungExpression, MAQCsubset, MetaGxBreast, MetaGxOvarian, miRNATarget, msd16s, mvoutData, Neve2006, PREDAsampledata, ProData, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, pumadata, rcellminerData, RUVnormalizeData, SpikeInSubset, TCGAcrcmiRNA, TCGAcrcmRNA, tweeDEseqCountData, yeastCC, coreheat, crmn, eLNNpairedCov, GWASbyCluster, heatmapFlex, lmQCM, MM2Sdata, MMDvariance, propOverlap
Imports Me	a4Base, a4Classif, a4Core, a4Preproc, ABarray, ACE, aCGH, adSplit, affyILM, AgiMicroRna, ANF, annmap, annotate, AnnotationHubData, annotationTools, arrayQualityMetrics, attract, ballgown, BASiCS, BayesKnockdown, BgeeDB, biobroom, bioCancer, biocViews, BioNet, biosigner, biscuiteer, BiSeq, blima, bnem, BreastSubtypeR, BSgenomeForge, bsseq, CAFE, canceR, Cardinal, CellTrails, cfdnakit, CGHnormaliter, ChIPQC, ChIPXpress, ChromHeatMap, cicero, clipper, CluMSID, cn.mops, COCOA, cogena, combi, CompoundDb, ConsensusClusterPlus, consensusOV, coRdon, CoreGx, crlmm, cyanoFilter, cycle, cydar, CytoML, DAPAR, ddCt, DEGreport, DESeq2, destiny, DExMA, discordant, easyRNASeq, EBarrays, ecolitk, EGAD, ensembldb, EpiMix, esetVis, ExiMiR, ffpe, findIPs, flowClust, flowCore, flowFP, flowMatch, flowMeans, flowSpecs, flowStats, flowViz, flowWorkspace, FRASER, frma, frmaTools, gCrisprTools, gcrma, gemma.R, geneClassifiers, GeneExpressionSignature, genefilter, GeneMeta, geneRecommender, GeneRegionScan, GENESIS, GenomicInteractions, GenomicScores, GenomicSuperSignature, GEOsubmission, gep2pep, ggbio, GlobalAncova, globaltest, gmapR, GSRI, GSVA, Gviz, HEM, hermes, HTqPCR, HTSFilter, infinityFlow, IsoformSwitchAnalyzeR, isomiRs, katdetectr, kissDE, LiquidAssociation, LRBaseDbi, makecdfenv, MAPFX, maSigPro, MAST, mastR, mBPCR, MeSHDbi, metaseqR2, MethylAid, methylCC, methylclock, methylumi, MiChip, microbiomeDASim, minfi, MinimumDistance, MiPP, MIRA, miRSM, missMethyl, MLSeq, mogsa, Moonlight2R, MoonlightR, MSnID, MultiAssayExperiment, MultiRNAflow, multiscan, mzR, npGSEA, nucleR, OAtools, oligoClasses, omicade4, omicsViewer, omXplore, ontoProc, openCyto, oposSOM, oppar, OrganismDbi, panp, phantasus, phantasusLite, PharmacoGx, phyloseq, piano, plgem, plier, podkat, prebs, PrInCE, proBatch, progeny, pRoloc, PROMISE, PRONE, PROPS, Prostar, protGear, ptairMS, puma, PureCN, pvac, pvca, qcmetrics, QDNAseq, QFeatures, qpgraph, quantiseqr, quantro, QuasR, qusage, RadioGx, randPack, ReactomeGSA, RIVER, Rmagpie, RMassBank, RNAseqCovarImpute, roastgsa, rols, ropls, ROTS, rqubic, rScudo, Rtpca, RUVnormalize, scmap, scTGIF, SeqVarTools, shinyMethyl, ShortRead, SigsPack, sigsquared, singscore, sitadela, sketchR, SmartPhos, SomaticSignatures, SpatialDecon, SpatialFeatureExperiment, SpatialOmicsOverlay, spkTools, SplineDV, SPONGE, standR, STATegRa, subSeq, TDbasedUFEadv, TEQC, TFBSTools, tidyFlowCore, timecourse, TMixClust, TnT, topdownr, ToxicoGx, tradeSeq, TTMap, twilight, txdbmaker, uSORT, VanillaICE, variancePartition, VariantAnnotation, VariantFiltering, VariantTools, vidger, vulcan, wateRmelon, wpm, xcms, Xeva, BloodCancerMultiOmics2017, DeSousa2013, DExMAdata, Fletcher2013a, GSE13015, hgu133plus2CellScore, IHWpaper, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, mcsurvdata, pRolocdata, seqc, signatureSearchData, ExpHunterSuite, ExpressionNormalizationWorkflow, GeoMxWorkflows, AnnoProbe, bapred, BioUtils, CIARA, ClassComparison, ClassDiscovery, D4TAlink.light, FMradio, geneExpressionFromGEO, GSEMA, IntegratedJM, maGUI, nlcv, NMF, PCAPAM50, RCPA, RobLox, RPPanalyzer, ssizeRNA, TailRank
Suggests Me	AUCell, autonomics, BiocGenerics, CellMapper, clustComp, ClusterGVis, coseq, cypress, dar, DART, dcanr, dearseq, DeconvoBuddies, DspikeIn, edgeR, EnMCB, EpiDISH, epivizr, epivizrChart, epivizrStandalone, genefu, GENIE3, GenomicPlot, GenomicRanges, GSAR, GSgalgoR, Heatplus, kebabs, les, limma, M3Drop, mCSEA, messina, mitology, MOSim, msa, multiClust, OSAT, pathMED, PCAtools, PLSDAbatch, RFGeneRank, ribosomeProfilingQC, ROC, RTCGA, scater, scmeth, SeqArray, sparrow, spatialHeatmap, stageR, survcomp, TargetScore, TCGAbiolinks, TFutils, tkWidgets, TOP, vbmp, widgetTools, biotmleData, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, dorothea, dyebiasexamples, HMP16SData, HMP2Data, mammaPrintData, mtbls2, RegParallel, rheumaticConditionWOLLBOLD, seventyGeneData, yeastExpData, yeastRNASeq, amap, aroma.affymetrix, BaseSet, CimpleG, clValid, CrossValidate, distrDoc, GenAlgo, ggpicrust2, hexbin, HTSCluster, isatabr, MetabolSSMF, mi4p, Modeler, MosaiClusteR, multiclassPairs, NACHO, omicsTools, ordinalbayes, Patterns, rsconnect, Seurat, sigminer, SomaDataIO, tinyarray
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	Biobase_2.72.0.tar.gz
Windows Binary (x86_64)	Biobase_2.72.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	Biobase_2.72.0.tgz
macOS Binary (sonoma-arm64)	Biobase_2.72.0.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