Biobase

DOI: 10.18129/B9.bioc.Biobase    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Biobase.

Biobase: Base functions for Bioconductor

Bioconductor version: 3.13

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 "4.1") and enter:

if (!requireNamespace("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 2.52.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 16.5 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, affyQCReport, AGDEX, AgiMicroRna, AIMS, ALL, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, antiProfilesData, ArrayExpress, arrayMvout, ArrayTools, Autotuner, BAGS, bcellViper, beadarray, beadarrayExampleData, beadarraySNP, bgx, BicARE, bigmelon, BiocCaseStudies, bioDist, BioMVCClass, BioQC, biosigner, bladderbatch, BLMA, BrainStars, brgedata, CAMERA, cancerclass, cancerdata, casper, Category, categoryCompare, CCl4, CCPROMISE, cellHTS2, ceu1kg, ceuhm3, 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, dsQTL, DSS, dualKS, dyebias, EBarrays, EDASeq, edge, EGSEA, eisa, epigenomix, epivizrData, etec16s, EuPathDB, ExiMiR, ExpressionAtlas, fabia, fabiaData, factDesign, fastseg, fibroEset, flowBeads, frma, gaga, gaschYHS, GeneAnswers, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, geNetClassifier, GEOquery, GOexpress, golubEsets, goProfiles, GOstats, GSE13015, GSE62944, GSEABase, GSEABenchmarkeR, GSEAlm, GSVAdata, GWASTools, hapFabia, harbChIP, HELP, Hiiragi2013, hmyriB36, hopach, HTqPCR, HumanAffyData, humanStemCell, HybridMTest, iBMQ, iCheck, IdeoViz, idiogram, InPAS, INSPEcT, isobar, iterativeBMA, IVAS, Iyer517, kidpack, leeBamViews, leukemiasEset, lumi, lumiBarnes, lungExpression, macat, made4, maEndToEnd, mAPKL, MAQCsubset, MAQCsubsetAFX, MAQCsubsetILM, massiR, MEAL, metabomxtr, metagenomeFeatures, metagenomeSeq, MetaGxBreast, MetaGxOvarian, metavizr, MethPed, methyAnalysis, methylumi, Mfuzz, MiChip, microbiomeExplorer, mimager, MIMOSA, MineICA, MiRaGE, miRcomp, miRNATarget, MLInterfaces, MMDiff2, monocle, msd16s, MSnbase, Mulcom, MultiDataSet, multtest, mvoutData, NanoStringDiff, NanoStringNCTools, Neve2006, NOISeq, nondetects, normalize450K, NormqPCR, oligo, omicRexposome, OrderedList, OTUbase, OutlierD, PADOG, pandaR, panp, pcaMethods, pcot2, 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, rnaSeqMap, Rnits, ropls, RTCA, RTopper, RUVnormalizeData, RUVSeq, safe, SCAN.UPC, SeqGSEA, SigCheck, siggenes, simulatorZ, singleCellTK, SpeCond, SPEM, SpikeInSubset, spkTools, splineTimeR, STROMA4, SummarizedExperiment, TCGAcrcmiRNA, TCGAcrcmRNA, TDARACNE, tigre, tilingArray, topGO, TPP, tRanslatome, tspair, tweeDEseqCountData, twilight, UNDO, variancePartition, VegaMC, viper, vsn, wateRmelon, webbioc, XDE, yarn, yeastCC
Imports Me a4Base, a4Classif, a4Core, a4Preproc, ABarray, ACE, aCGH, adSplit, affyILM, affyQCReport, AgiMicroRna, ANF, annmap, annotate, AnnotationHubData, annotationTools, ArrayExpressHTS, arrayQualityMetrics, ArrayTools, attract, ballgown, BASiCS, BayesKnockdown, BgeeDB, biobroom, bioCancer, biocViews, BioNet, biscuiteer, BiSeq, blima, BloodCancerMultiOmics2017, bnem, BrainStars, bsseq, BubbleTree, CAFE, canceR, Cardinal, ccTutorial, CellScore, CellTrails, ceu1kgv, cgdv17, CGHnormaliter, ChIPQC, ChIPXpress, ChromHeatMap, chromswitch, cicero, clipper, CluMSID, cn.mops, COCOA, coexnet, cogena, combi, conclus, ConsensusClusterPlus, consensusDE, consensusOV, coRdon, CoreGx, crlmm, CrossICC, 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, exomePeak2, ExpHunterSuite, ExpressionNormalizationWorkflow, farms, ffpe, FindMyFriends, 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, GeomxTools, GEOsubmission, gep2pep, gespeR, ggbio, girafe, GISPA, GlobalAncova, globaltest, gmapR, GSE13015, GSRI, GSVA, Gviz, Harshlight, HEM, hgu133plus2CellScore, HTqPCR, HTSFilter, IHWpaper, imageHTS, ImmuneSpaceR, infinityFlow, InTAD, IsoformSwitchAnalyzeR, IsoGeneGUI, isomiRs, iterClust, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, kissDE, lapmix, LiquidAssociation, LRBaseDbi, maanova, MAGeCKFlute, makecdfenv, maSigPro, MAST, mBPCR, mcsurvdata, MeSHDbi, metaseqR2, methyAnalysis, MethylAid, methylCC, methylumi, mfa, MiChip, microbiomeDASim, MIGSA, minfi, MinimumDistance, MiPP, MIRA, miRSM, missMethyl, MLSeq, MMAPPR2, mogsa, MoonlightR, MOSim, MSEADbi, MSnID, MultiAssayExperiment, multiscan, mzR, NanoStringQCPro, ncdfFlow, NormalyzerDE, npGSEA, nucleR, oligoClasses, omicade4, ontoProc, openCyto, oposSOM, oppar, OrganismDbi, panp, PCpheno, phantasus, PharmacoGx, phemd, phyloseq, piano, plethy, plgem, plier, podkat, POST, ppiStats, prebs, PrInCE, proBatch, proFIA, progeny, pRoloc, pRolocdata, PROMISE, PROPS, ProteomicsAnnotationHubData, PSEA, psygenet2r, ptairMS, puma, pvac, pvca, pwOmics, qcmetrics, QDNAseq, QFeatures, qpgraph, quantiseqr, quantro, QuasR, qusage, RadioGx, randPack, ReportingTools, restfulSE, RGalaxy, RIVER, Rmagpie, RMassBank, RNAinteract, RNAinteractMAPK, rols, ROTS, RpsiXML, rqubic, rScudo, Rtpca, Rtreemix, RUVnormalize, SAGx, scmap, scTGIF, seqc, SeqVarTools, ShortRead, signatureSearchData, SigsPack, sigsquared, SimBindProfiles, singscore, sitadela, SLGI, SMITE, SomaticSignatures, spkTools, SPONGE, STATegRa, subSeq, synapter, TEQC, TFBSTools, timecourse, TMixClust, TnT, ToPASeq, topdownr, ToxicoGx, tradeSeq, TTMap, twilight, uSORT, VanillaICE, VariantAnnotation, VariantFiltering, VariantTools, vidger, vulcan, wateRmelon, wpm, XBSeq, xcms, Xeva, yri1kgv
Suggests Me AUCell, BiocCaseStudies, 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, POMA, RcisTarget, ReactomeGSA, RegParallel, rheumaticConditionWOLLBOLD, ROC, RTCGA, scater, scmeth, scran, SeqArray, seventyGeneData, slinky, 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_2.52.0.tar.gz
Windows Binary Biobase_2.52.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) Biobase_2.52.0.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

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