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Biobase (development version)

Biobase

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

Biobase: Base functions for Bioconductor

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DOI: 10.18129/B9.bioc.Biobase

Bioconductor version: Development (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")):

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Infrastructure, Software

Version 2.71.0

In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20.5 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, affyContam, affycoretools, affyPLM, AGDEX, AIMS, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, ArrayExpress, arrayMvout, BAGS, bandle, BicARE, bigmelon, BioMVCClass, BioQC, BLMA, borealis, CAMERA, cancerclass, 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, 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, MethPed, methylumi, Mfuzz, MiChip, 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, 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, bladderbatch, brgedata, cancerdata, CCl4, CLL, colonCA, CRCL18, curatedBreastData, curatedOvarianData, davidTiling, diggitdata, DLBCL, dressCheck, etec16s, fabiaData, fibroEset, gaschYHS, golubEsets, GSE103322, GSE13015, GSE62944, GSVAdata, harbChIP, HumanAffyData, humanStemCell, Iyer517, kidpack, leeBamViews, leukemiasEset, lumiBarnes, lungExpression, MAQCsubset, MetaGxBreast, miRNATarget, msd16s, mvoutData, Neve2006, PREDAsampledata, ProData, prostateCancerCamcap, prostateCancerGrasso, prostateCancerStockholm, prostateCancerTaylor, prostateCancerVarambally, pumadata, rcellminerData, RUVnormalizeData, SpikeInSubset, TCGAcrcmiRNA, TCGAcrcmRNA, tweeDEseqCountData, yeastCC, crmn, dGAselID, eLNNpairedCov, GWASbyCluster, heatmapFlex, lmQCM, MM2Sdata, MMDvariance, propOverlap

Imports Me a4Base, a4Classif, a4Core, a4Preproc, ABarray, ACE, aCGH, adSplit, affyILM, AgiMicroRna, ANF, annmap, annotate, AnnotationHubData, annotationTools, attract, ballgown, BASiCS, BayesKnockdown, BgeeDB, biobroom, bioCancer, biocViews, BioNet, biosigner, biscuiteer, BiSeq, bnem, BreastSubtypeR, BSgenomeForge, bsseq, CAFE, canceR, Cardinal, CellTrails, cfdnakit, CGHnormaliter, 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, frma, frmaTools, gCrisprTools, gcrma, gemma.R, geneClassifiers, GeneExpressionSignature, genefilter, GeneMeta, geneRecommender, GeneRegionScan, GenomicInteractions, GenomicScores, GenomicSuperSignature, GEOsubmission, gep2pep, ggbio, GlobalAncova, globaltest, GSRI, GSVA, Gviz, HEM, hermes, HTqPCR, HTSFilter, infinityFlow, IsoformSwitchAnalyzeR, katdetectr, kissDE, LiquidAssociation, LRBaseDbi, makecdfenv, MAPFX, maSigPro, MAST, mastR, mBPCR, MeSHDbi, metaseqR2, MethylAid, methylCC, methylclock, methylumi, MiChip, minfi, MinimumDistance, MiPP, MIRA, miRSM, missMethyl, MLSeq, mogsa, Moonlight2R, MoonlightR, MSnID, MultiAssayExperiment, MultiRNAflow, multiscan, mzR, npGSEA, nucleR, oligoClasses, omicade4, omicsViewer, ontoProc, openCyto, oposSOM, oppar, OrganismDbi, panp, phantasus, phantasusLite, PharmacoGx, phyloseq, piano, plgem, plier, PLSDAbatch, podkat, prebs, PrInCE, 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, ropls, ROTS, rqubic, rScudo, Rtpca, RUVnormalize, scmap, scTGIF, shinyMethyl, ShortRead, SigsPack, sigsquared, singscore, sitadela, sketchR, SomaticSignatures, SpatialDecon, SpatialFeatureExperiment, SpatialOmicsOverlay, spkTools, SplineDV, SPONGE, standR, STATegRa, subSeq, TDbasedUFEadv, TEQC, TFBSTools, tidyFlowCore, timecourse, TMixClust, TnT, topdownr, ToxicoGx, tradeSeq, TTMap, twilight, txdbmaker, UPDhmm, uSORT, VanillaICE, variancePartition, VariantAnnotation, VariantFiltering, vidger, wateRmelon, wpm, xcms, Xeva, BloodCancerMultiOmics2017, DeSousa2013, DExMAdata, Fletcher2013a, GSE13015, hgu133plus2CellScore, Hiiragi2013, IHWpaper, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, mcsurvdata, pRolocdata, seqc, signatureSearchData, ExpressionNormalizationWorkflow, GeoMxWorkflows, AnnoProbe, bapred, CIARA, ClassComparison, ClassDiscovery, D4TAlink.light, FMradio, geneExpressionFromGEO, GSEMA, IntegratedJM, maGUI, nlcv, NMF, PCAPAM50, RCPA, RobLox, RPPanalyzer, SCdeconR, scPOEM, 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, ribosomeProfilingQC, ROC, RTCGA, scater, scmeth, sparrow, 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, evanverse, GenAlgo, ggpicrust2, hexbin, HTSCluster, isatabr, MetabolSSMF, mi4p, Modeler, multiclassPairs, NACHO, 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_2.71.0.tar.gz

Windows Binary (x86_64) Biobase_2.71.0.zip (64-bit only)

macOS Binary (x86_64) Biobase_2.71.0.tgz

macOS Binary (arm64) Biobase_2.71.0.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