Registration and Call for Abstracts Open for Bioc2024

Biobase

This is the development version of Biobase; for the stable release version, see Biobase.

Biobase: Base functions for Bioconductor


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Infrastructure, Software
Version 2.63.1
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 https://bioconductor.org/packages/Biobase
Bug Reports https://github.com/Bioconductor/Biobase/issues
See More
Suggests tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma
Linking To
Enhances
Depends On Me ACME, affy, affycomp, affycompData, affyContam, affycoretools, affyPLM, AGDEX, AgiMicroRna, AIMS, ALL, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, antiProfilesData, ArrayExpress, arrayMvout, BAGS, bandle, bcellViper, beadarray, beadarrayExampleData, beadarraySNP, bgx, BicARE, bigmelon, bioDist, BioMVCClass, BioQC, bladderbatch, BLMA, borealis, brgedata, CAMERA, cancerclass, cancerdata, casper, Category, categoryCompare, CCl4, CCPROMISE, cellHTS2, CGHbase, CGHcall, CGHregions, clippda, CLL, clusterStab, CMA, cn.farms, codelink, colonCA, convert, copa, covEB, covRNA, CRCL18, curatedBreastData, curatedOvarianData, davidTiling, DEXSeq, DFP, diggit, diggitdata, DLBCL, doppelgangR, dressCheck, DSS, dyebias, EBarrays, EDASeq, edge, EGSEA, epigenomix, epivizrData, etec16s, EuPathDB, ExiMiR, ExpressionAtlas, fabia, fabiaData, factDesign, fastseg, fibroEset, flowBeads, frma, gaga, gaschYHS, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, geNetClassifier, GeoDiff, GEOexplorer, GeomxTools, GEOquery, GOexpress, golubEsets, goProfiles, GOstats, GSE103322, GSE13015, GSE62944, GSEABase, GSEABenchmarkeR, GSEAlm, GSVAdata, GWASTools, hapFabia, harbChIP, HELP, Hiiragi2013, hopach, HTqPCR, HumanAffyData, humanStemCell, HybridMTest, iBMQ, iCheck, IdeoViz, idiogram, INSPEcT, isobar, iterativeBMA, IVAS, Iyer517, kidpack, leeBamViews, leukemiasEset, lumi, lumiBarnes, lungExpression, made4, maEndToEnd, MAQCsubset, massiR, MEAL, metabomxtr, metagenomeSeq, MetaGxBreast, MetaGxOvarian, MethPed, methylumi, Mfuzz, MiChip, microbiomeExplorer, mimager, MineICA, MiRaGE, miRcomp, miRNATarget, MLInterfaces, MMDiff2, monocle, msd16s, MSnbase, Mulcom, MultiDataSet, multtest, mvoutData, NanoStringDiff, NanoStringNCTools, NanoTube, Neve2006, NOISeq, nondetects, normalize450K, NormqPCR, octad, oligo, omicRexposome, OrderedList, OTUbase, PADOG, pandaR, panp, pcaMethods, pdInfoBuilder, pepStat, phenoTest, PLPE, POWSC, PREDA, PREDAsampledata, ProData, pRolocGUI, PROMISE, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, pumadata, qpcrNorm, qPLEXanalyzer, R453Plus1Toolbox, RbcBook1, rbsurv, rcellminer, rcellminerData, ReadqPCR, RefPlus, rexposome, Risa, Rmagpie, Rnits, RTCA, RTopper, RUVnormalizeData, RUVSeq, safe, SCAN.UPC, SeqGSEA, SigCheck, siggenes, singleCellTK, SpeCond, SPEM, SpikeInSubset, spkTools, splineTimeR, STROMA4, SummarizedExperiment, TCGAcrcmiRNA, TCGAcrcmRNA, tigre, tilingArray, topGO, TPP, tRanslatome, tweeDEseqCountData, twilight, UNDO, VegaMC, viper, vsn, wateRmelon, webbioc, XDE, yarn, yeastCC
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, BloodCancerMultiOmics2017, bnem, BSgenomeForge, bsseq, BubbleTree, CAFE, canceR, Cardinal, CellScore, CellTrails, cfdnakit, CGHnormaliter, ChIPQC, ChIPXpress, ChromHeatMap, cicero, clipper, CluMSID, cn.mops, COCOA, cogena, combi, CompoundDb, ConsensusClusterPlus, consensusDE, consensusOV, coRdon, CoreGx, crlmm, crossmeta, cummeRbund, cyanoFilter, cycle, cydar, CytoML, DAPAR, ddCt, debCAM, DEGreport, DESeq2, DeSousa2013, destiny, DExMA, DExMAdata, discordant, easyRNASeq, EBarrays, ecolitk, EGAD, ENmix, ensembldb, EpiMix, erma, esetVis, ExiMiR, ExpHunterSuite, ExpressionNormalizationWorkflow, farms, ffpe, Fletcher2013a, 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, GeoMxWorkflows, GEOsubmission, gep2pep, gespeR, ggbio, girafe, GlobalAncova, globaltest, gmapR, GSE13015, GSRI, GSVA, Gviz, Harshlight, HEM, hermes, hgu133plus2CellScore, HTqPCR, HTSFilter, IHWpaper, ImmuneSpaceR, infinityFlow, InPAS, InTAD, IsoformSwitchAnalyzeR, isomiRs, iterClust, katdetectr, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, kissDE, lapmix, LiquidAssociation, LRBaseDbi, lute, MAGeCKFlute, makecdfenv, maSigPro, MAST, mastR, mBPCR, mcsurvdata, MeSHDbi, metaseqR2, MethylAid, methylCC, methylclock, methylumi, mfa, MiChip, microbiomeDASim, microbiomeMarker, minfi, MinimumDistance, MiPP, MIRA, miRSM, missMethyl, MLSeq, MMAPPR2, mogsa, Moonlight2R, MoonlightR, MSnID, MultiAssayExperiment, MultiRNAflow, multiscan, mzR, ncdfFlow, netZooR, NormalyzerDE, npGSEA, nucleR, oligoClasses, omicade4, omicsViewer, ontoProc, openCyto, oposSOM, oppar, OrganismDbi, panp, phantasus, phantasusLite, PharmacoGx, phemd, phenomis, phyloseq, piano, plgem, plier, PLSDAbatch, podkat, prebs, PrInCE, progeny, pRoloc, pRolocdata, PROMISE, PROPS, Prostar, protGear, PSEA, psygenet2r, ptairMS, puma, PureCN, pvac, pvca, pwOmics, qcmetrics, QDNAseq, QFeatures, qpgraph, quantiseqr, quantro, QuasR, qusage, RadioGx, randPack, ReactomeGSA, ReportingTools, restfulSE, RIVER, Rmagpie, RMassBank, RNAinteract, RNAinteractMAPK, RNAseqCovarImpute, roastgsa, rols, ropls, ROTS, rqubic, rScudo, Rtpca, Rtreemix, RUVnormalize, scmap, scTGIF, seqc, SeqVarTools, shinyMethyl, ShortRead, signatureSearchData, SigsPack, sigsquared, SimBindProfiles, singscore, sitadela, sketchR, SMITE, SomaticSignatures, SpatialDecon, SpatialOmicsOverlay, spkTools, SPONGE, standR, STATegRa, subSeq, synapter, TDbasedUFEadv, TEQC, TFBSTools, timecourse, TMixClust, TnT, topdownr, ToxicoGx, tradeSeq, traviz, TTMap, twilight, txdbmaker, uSORT, VanillaICE, variancePartition, VariantAnnotation, VariantFiltering, VariantTools, vidger, vulcan, wateRmelon, wpm, xcms, Xeva
Suggests Me AUCell, BiocCheck, BiocGenerics, BiocOncoTK, biotmleData, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, CellMapper, clustComp, coseq, cypress, dar, DART, dcanr, dearseq, dorothea, dyebiasexamples, edgeR, EnMCB, EpiDISH, epivizr, epivizrChart, epivizrStandalone, farms, genefu, GENIE3, GenomicPlot, GenomicRanges, GSAR, GSgalgoR, Heatplus, HMP16SData, HMP2Data, interactiveDisplay, kebabs, les, limma, M3Drop, mammaPrintData, mCSEA, messina, MOSim, msa, multiClust, OSAT, PCAtools, RcisTarget, RegParallel, rheumaticConditionWOLLBOLD, ribosomeProfilingQC, ROC, RTCGA, scater, scmeth, SeqArray, seventyGeneData, sparrow, spatialHeatmap, stageR, survcomp, TargetScore, TCGAbiolinks, TFutils, tkWidgets, TOP, 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_2.63.1.tar.gz
Windows Binary Biobase_2.63.1.zip
macOS Binary (x86_64) Biobase_2.63.1.tgz
macOS Binary (arm64) Biobase_2.63.1.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