Biobase

DOI: 10.18129/B9.bioc.Biobase    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see Biobase.

Biobase: Base functions for Bioconductor

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Infrastructure, Software
Version	2.56.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 17.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), BiocGenerics(>= 0.27.1), utils
Imports	methods
LinkingTo
Suggests	tools, tkWidgets, ALL, RUnit, golubEsets
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/Biobase
BugReports	https://github.com/Bioconductor/Biobase/issues
Depends On Me	ACME, affy, affycomp, affycompData, affyContam, affycoretools, affyPLM, AGDEX, AgiMicroRna, AIMS, ALL, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, antiProfilesData, ArrayExpress, arrayMvout, Autotuner, 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, 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, macat, made4, maEndToEnd, mAPKL, MAQCsubset, MAQCsubsetILM, massiR, MEAL, metabomxtr, metagenomeSeq, MetaGxBreast, MetaGxOvarian, metavizr, MethPed, methylumi, Mfuzz, MiChip, microbiomeExplorer, mimager, MIMOSA, MineICA, MiRaGE, miRcomp, miRNATarget, MLInterfaces, MMDiff2, monocle, msd16s, MSnbase, Mulcom, MultiDataSet, multtest, mvoutData, NanoStringDiff, NanoStringNCTools, NanoTube, Neve2006, NOISeq, nondetects, normalize450K, NormqPCR, 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, Ringo, Risa, Rmagpie, Rnits, RTCA, RTopper, RUVnormalizeData, RUVSeq, safe, SCAN.UPC, SeqGSEA, SigCheck, siggenes, singleCellTK, SpeCond, SPEM, SpikeInSubset, spkTools, splineTimeR, STROMA4, SummarizedExperiment, TCGAcrcmiRNA, TCGAcrcmRNA, TDARACNE, tigre, tilingArray, topGO, TPP, tRanslatome, tspair, 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, ArrayExpressHTS, arrayQualityMetrics, attract, ballgown, BASiCS, BayesKnockdown, BgeeDB, biobroom, bioCancer, biocViews, BioNet, biosigner, biscuiteer, BiSeq, blima, BloodCancerMultiOmics2017, bnem, bsseq, BubbleTree, CAFE, canceR, Cardinal, ccTutorial, CellScore, CellTrails, CGHnormaliter, ChIPQC, ChIPXpress, ChromHeatMap, chromswitch, cicero, clipper, CluMSID, cn.mops, COCOA, coexnet, cogena, combi, CompoundDb, conclus, ConsensusClusterPlus, consensusDE, consensusOV, coRdon, CoreGx, crlmm, crossmeta, ctgGEM, cummeRbund, cyanoFilter, cycle, cydar, CytoML, CytoTree, DAPAR, ddCt, debCAM, deco, DEGreport, DESeq2, DeSousa2013, destiny, DExMA, DExMAdata, diffloop, discordant, easyRNASeq, EBarrays, ecolitk, EGAD, ENmix, ensembldb, erma, esetVis, ExiMiR, ExpHunterSuite, ExpressionNormalizationWorkflow, farms, ffpe, Fletcher2013a, flowClust, flowCore, flowFP, flowMatch, flowMeans, flowSpecs, flowStats, flowUtils, flowViz, flowWorkspace, FRASER, frma, frmaTools, GAPGOM, gCrisprTools, gcrma, GCSscore, genbankr, geneClassifiers, GeneExpressionSignature, genefilter, GeneMeta, geneRecommender, GeneRegionScan, GENESIS, GenomicFeatures, GenomicInteractions, GenomicScores, GenomicSuperSignature, GeoMxWorkflows, GEOsubmission, gep2pep, gespeR, ggbio, girafe, GISPA, GlobalAncova, globaltest, gmapR, GSE13015, GSRI, GSVA, Gviz, Harshlight, HEM, hermes, hgu133plus2CellScore, HTqPCR, HTSFilter, IHWpaper, imageHTS, ImmuneSpaceR, infinityFlow, InPAS, InTAD, IsoformSwitchAnalyzeR, IsoGeneGUI, isomiRs, iterClust, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, kissDE, lapmix, LiquidAssociation, LRBaseDbi, maanova, MAGeCKFlute, makecdfenv, maSigPro, MAST, mBPCR, mcsurvdata, MeSHDbi, metaseqR2, MethylAid, methylCC, methylclock, methylumi, mfa, MiChip, microbiomeDASim, microbiomeMarker, MIGSA, minfi, MinimumDistance, MiPP, MIRA, miRSM, missMethyl, MLSeq, MMAPPR2, mogsa, MoonlightR, MOSim, MSnID, MultiAssayExperiment, multiscan, mzR, NanoStringQCPro, ncdfFlow, netZooR, NormalyzerDE, npGSEA, nucleR, oligoClasses, omicade4, omicsViewer, ontoProc, openCyto, oposSOM, oppar, OrganismDbi, panp, phantasus, PharmacoGx, phemd, phyloseq, piano, plethy, plgem, plier, podkat, ppiStats, prebs, PrInCE, proBatch, proFIA, progeny, pRoloc, pRolocdata, PROMISE, PROPS, ProteomicsAnnotationHubData, protGear, PSEA, psygenet2r, ptairMS, puma, PureCN, pvac, pvca, pwOmics, qcmetrics, QDNAseq, QFeatures, qpgraph, quantiseqr, quantro, QuasR, qusage, RadioGx, randPack, ReportingTools, restfulSE, RIVER, Rmagpie, RMassBank, RNAinteract, RNAinteractMAPK, rols, ropls, ROTS, RpsiXML, rqubic, rScudo, Rtpca, Rtreemix, RUVnormalize, scmap, scTGIF, seqc, SeqVarTools, ShortRead, signatureSearchData, SigsPack, sigsquared, SimBindProfiles, singscore, sitadela, SLGI, SMITE, SomaticSignatures, SpatialDecon, spkTools, SPONGE, standR, STATegRa, subSeq, synapter, TEQC, TFBSTools, timecourse, TMixClust, TnT, topdownr, ToxicoGx, tradeSeq, traviz, TTMap, twilight, 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, BSgenome, ccTutorial, CellMapper, cellTree, clustComp, coseq, CountClust, DART, dcanr, dearseq, dorothea, dyebiasexamples, edgeR, EnMCB, EpiDISH, epivizr, epivizrChart, epivizrStandalone, farms, genefu, GENIE3, GenomicRanges, GSAR, GSgalgoR, Heatplus, HMP16SData, HMP2Data, interactiveDisplay, kebabs, les, limma, M3Drop, mammaPrintData, mAPKLData, mCSEA, messina, msa, multiClust, OSAT, PCAtools, pkgDepTools, RcisTarget, ReactomeGSA, RegParallel, rheumaticConditionWOLLBOLD, ROC, RTCGA, scater, scmeth, scran, SeqArray, seventyGeneData, sparrow, spatialHeatmap, stageR, survcomp, TargetScore, TCGAbiolinks, TFutils, TimeSeriesExperiment, tkWidgets, TypeInfo, vbmp, widgetTools, yeastExpData, yeastRNASeq
Links To Me
Build Report

Package Archives

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

Source Package	Biobase_2.56.0.tar.gz
Windows Binary	Biobase_2.56.0.zip (64-bit only)
macOS Binary (x86_64)	Biobase_2.56.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Biobase
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Biobase
Package Short Url	https://bioconductor.org/packages/Biobase/
Package Downloads Report	Download Stats