Biobase Package In R Download
DOI: 10.18129/B9.bioc.Biobase 
Biobase: Base functions for Bioconductor
Bioconductor version: Release (3.14)
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") | R Script | An introduction to Biobase and ExpressionSets | |
| R Script | esApply Introduction | |
| R Script | Notes for eSet developers | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Infrastructure, Software |
| Version | 2.54.0 |
| 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, AGDEX, AgiMicroRna, AIMS, ALL, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, antiProfilesData, ArrayExpress, arrayMvout, Autotuner, BAGS, bcellViper, beadarray, beadarrayExampleData, beadarraySNP, bgx, BicARE, bigmelon, bioDist, BioMVCClass, BioQC, biosigner, bladderbatch, BLMA, BrainStars, 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, dualKS, dyebias, EBarrays, EDASeq, edge, EGSEA, epigenomix, epivizrData, etec16s, EuPathDB, ExiMiR, ExpressionAtlas, fabia, fabiaData, factDesign, fastseg, fibroEset, flowBeads, frma, gaga, gaschYHS, GeneAnswers, 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, InPAS, 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, ropls, 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, biscuiteer, BiSeq, blima, BloodCancerMultiOmics2017, bnem, BrainStars, bsseq, BubbleTree, CAFE, canceR, Cardinal, ccTutorial, CellScore, CellTrails, CGHnormaliter, ChIPQC, ChIPXpress, ChromHeatMap, chromswitch, cicero, clipper, CluMSID, cn.mops, COCOA, coexnet, cogena, combi, 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, 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, GeoMxWorkflows, 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, 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, NormalyzerDE, npGSEA, nucleR, oligoClasses, omicade4, 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, PSEA, psygenet2r, ptairMS, puma, PureCN, 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, scmap, scTGIF, seqc, SeqVarTools, ShortRead, signatureSearchData, SigsPack, sigsquared, SimBindProfiles, singscore, sitadela, SLGI, SMITE, SomaticSignatures, SpatialDecon, spkTools, SPONGE, 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, POMA, RcisTarget, ReactomeGSA, RegParallel, rheumaticConditionWOLLBOLD, ROC, RTCGA, scater, scmeth, scran, SeqArray, seventyGeneData, slinky, 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_2.54.0.tar.gz |
| Windows Binary | Biobase_2.54.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | Biobase_2.54.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |
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