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BiocGenerics

S4 generic functions used in Bioconductor


Bioconductor version: Release (3.18)

The package defines many S4 generic functions used in Bioconductor.

Author: The Bioconductor Dev Team

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("BiocGenerics")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("BiocGenerics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Infrastructure, Software
Version 0.48.1
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, utils, graphics, stats
Imports methods, utils, graphics, stats
System Requirements
URL https://bioconductor.org/packages/BiocGenerics
Bug Reports https://github.com/Bioconductor/BiocGenerics/issues
See More
Suggests Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit
Linking To
Enhances
Depends On Me ACME, affy, affyPLM, altcdfenvs, amplican, AnnotationDbi, AnnotationForge, AnnotationHub, ATACseqQC, beadarray, bioassayR, Biobase, Biostrings, bnbc, BSgenome, BSgenomeForge, bsseq, Cardinal, Category, categoryCompare, ChAMPdata, chipseq, ChIPseqR, ChromHeatMap, clusterExperiment, codelink, consensusDE, consensusSeekeR, CoreGx, CRISPRseek, cummeRbund, DelayedArray, ensembldb, ensemblVEP, ExperimentHub, ExperimentHubData, GDSArray, geneplotter, GenomeInfoDb, genomeIntervals, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges, GenomicScores, ggbio, girafe, graph, GSEABase, GUIDEseq, HelloRanges, interactiveDisplay, interactiveDisplayBase, IRanges, ISLET, liftOver, MBASED, MineICA, minfi, MLInterfaces, MotifDb, mpra, MSnbase, multtest, NADfinder, ngsReports, oligo, OrganismDbi, pandaR, plethy, plyranges, profileplyr, PWMEnrich, QSutils, RareVariantVis, REDseq, Repitools, RnBeads, RPA, rsbml, S4Arrays, S4Vectors, ShortRead, simplifyEnrichment, soGGi, SparseArray, spqn, StructuralVariantAnnotation, SummarizedBenchmark, svaNUMT, svaRetro, TEQC, tigre, topdownr, topGO, UNDO, UniProt.ws, updateObject, VanillaICE, VariantAnnotation, VariantFiltering, VCFArray, XVector, yamss
Imports Me a4Preproc, affycoretools, affylmGUI, alabaster.bumpy, alabaster.files, alabaster.matrix, alabaster.ranges, alabaster.se, AllelicImbalance, AneuFinder, annmap, annotate, AnnotationHubData, ASpli, ATACseqTFEA, atena, AUCell, autonomics, bambu, bamsignals, BASiCS, batchelor, beachmat, bigmelon, BiocBook, biocGraph, BiocHail, BiocIO, BiocSingular, biotmle, biovizBase, biscuiteer, BiSeq, blima, breakpointR, BrowserViz, BubbleTree, bumphunter, BUSpaRse, CAGEfightR, CAGEr, casper, celaref, CellaRepertorium, CellBench, cellHTS2, CellMixS, CellTrails, cfDNAPro, cghMCR, ChemmineDrugs, ChemmineOB, ChemmineR, ChIPComp, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPQC, ChIPseeker, chipseq, chromstaR, chromVAR, cicero, CircSeqAlignTk, clusterSeq, cn.mops, CNEr, CNVPanelizer, CNVRanger, COCOA, cola, compEpiTools, CompoundDb, contiBAIT, crisprBase, crisprBowtie, crisprBwa, crisprDesign, crisprScore, crisprViz, crlmm, crossmeta, csaw, cummeRbund, CuratedAtlasQueryR, curatedCRCData, curatedOvarianData, cydar, dada2, dagLogo, DAMEfinder, ddCt, decompTumor2Sig, deconvR, DEGreport, DelayedDataFrame, demuxSNP, derfinder, DEScan2, DESeq2, DESpace, destiny, DEWSeq, DEXSeq, diffcoexp, diffHic, DirichletMultinomial, DiscoRhythm, DNAfusion, dreamlet, DRIMSeq, DropletUtils, DrugVsDisease, easyRNASeq, EBImage, EDASeq, eiR, eisaR, enhancerHomologSearch, enrichTF, epialleleR, EpiCompare, epigenomix, epimutacions, epistack, EpiTxDb, epivizrChart, epivizrStandalone, erma, esATAC, exomePeak2, ExpHunterSuite, factR, FamAgg, fastseg, ffpe, FindIT2, FLAMES, flowBin, flowClust, flowCore, flowFP, FlowSOM, flowSpecs, flowStats, flowWorkspace, fmcsR, FRASER, frma, GA4GHclient, GA4GHshiny, gcapc, gDNAinRNAseqData, gDNAx, genbankr, geneAttribution, geneClassifiers, GENESIS, GenomAutomorphism, GenomicAlignments, GenomicInteractions, GenomicPlot, GenomicTuples, GenVisR, GeomxTools, GeoMxWorkflows, glmGamPoi, gmapR, gmoviz, goseq, GOTHiC, gpuMagic, Gviz, HDF5Array, heatmaps, hermes, HiCDOC, HiCExperiment, HiContacts, HiLDA, hiReadsProcessor, hopach, HTSeqGenie, icetea, igvR, IHW, IHWpaper, IMAS, infercnv, INSPEcT, InTAD, intansv, InteractionSet, IntEREst, IONiseR, iSEE, IsoformSwitchAnalyzeR, isomiRs, IVAS, KCsmart, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, ldblock, lemur, LinTInd, lisaClust, LOLA, mariner, maser, MAST, matter, MEAL, meshr, MetaboAnnotation, metaMS, metaseqR2, methInheritSim, MethylAid, methylPipe, methylumi, mia, miaViz, microbiomeDataSets, microbiomeMarker, miloR, mimager, MinimumDistance, MIRA, MiRaGE, missMethyl, MMAPPR2, Modstrings, mogsa, monaLisa, monocle, Motif2Site, motifbreakR, MouseGastrulationData, MouseThymusAgeing, msa, MsBackendSql, MSnID, MultiAssayExperiment, multicrispr, MultiDataSet, multiMiR, MultimodalExperiment, mumosa, MutationalPatterns, mzR, NanoStringNCTools, ncdfFlow, nearBynding, npGSEA, nucleR, oligoClasses, OmicsLonDA, openCyto, openPrimeR, ORFik, OUTRIDER, parglms, pcaMethods, PDATK, pdInfoBuilder, PharmacoGx, phemd, PhIPData, PhosR, phyloseq, Pi, piano, PING, plyinteractions, podkat, pram, primirTSS, proDA, profileScoreDist, pRoloc, pRolocGUI, ProteoDisco, PSMatch, PureCN, pwOmics, QFeatures, qPLEXanalyzer, qsea, QTLExperiment, QuasR, R3CPET, R453Plus1Toolbox, RadioGx, raer, raerdata, RaggedExperiment, ramr, ramwas, RCAS, RcisTarget, RCy3, RCyjs, recoup, REMP, ReportingTools, RGMQL, RGSEA, RiboCrypt, RiboDiPA, RiboProfiling, ribosomeProfilingQC, Ringo, RJMCMCNucleosomes, rnaEditr, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, roar, rols, Rqc, rqubic, Rsamtools, rsbml, rScudo, RTCGAToolbox, rtracklayer, SC3, SCArray.sat, scater, scDblFinder, scmap, SCnorm, SCOPE, scPipe, scran, scRNAseq, scruff, scuttle, SeqVarTools, sevenC, SGSeq, SharedObject, shinyMethyl, signatureSearch, signeR, signifinder, single, SingleCellExperiment, SingleMoleculeFootprinting, sitadela, SNPhood, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, snpStats, sparrow, SpatialExperiment, SpatialFeatureExperiment, spatialLIBD, spatzie, Spectra, spicyR, splatter, SpliceWiz, SplicingGraphs, SQLDataFrame, sRACIPE, sscu, standR, strandCheckR, Streamer, Structstrings, SummarizedExperiment, SynMut, systemPipeR, systemPipeRdata, tadar, TAPseq, target, TCGAutils, TCseq, TENxBUSData, TENxIO, TFBSTools, TitanCNA, ToxicoGx, trackViewer, transcriptR, transite, TransView, TreeSummarizedExperiment, tRNA, tRNAscanImport, TVTB, txcutr, Ularcirc, UMI4Cats, unifiedWMWqPCR, universalmotif, uSORT, VariantTools, VariantToolsData, velociraptor, wavClusteR, weitrix, xcms, XDE, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector
Suggests Me acde, adverSCarial, aggregateBioVar, AIMS, ASSET, ASURAT, BaalChIP, baySeq, BDMMAcorrect, bigmelon, bigPint, BiocCheck, BiocParallel, BiocStyle, biocViews, BioMM, biosigner, BiRewire, BLMA, BloodGen3Module, bnem, borealis, BUScorrect, BUSseq, CAFE, CAMERA, CancerSubtypes, CausalR, ccrepe, CDI, cellmigRation, CellNOptR, CexoR, chihaya, ChIPanalyser, ChIPXpress, CHRONOS, CINdex, cleanUpdTSeq, clipper, clustComp, CNORfeeder, CNORfuzzy, coMET, ConnectivityMap, consensus, cosmiq, COSNet, cpvSNP, DEsubs, DExMA, DMRcaller, DMRcate, ENCODExplorerData, EnhancedVolcano, ENmix, EpiMix, epiNEM, EventPointer, fCCAC, fcScan, fgga, FGNet, FieldEffectCrc, flowCut, flowTime, fmrs, GateFinder, gCrisprTools, gdsfmt, GEM, GeneNetworkBuilder, GeneOverlap, geneplast, geneplast.data, geneRxCluster, geNetClassifier, genomation, GEOquery, GeoTcgaData, GMRP, GOstats, GraphPAC, GreyListChIP, grndata, GSVA, GWASTools, h5vc, Harman, HarmanData, healthyControlsPresenceChecker, hiAnnotator, HiCDCPlus, hierGWAS, HIREewas, HPiP, hypergraph, iCARE, iClusterPlus, IFAA, illuminaio, immunotation, InPAS, INPower, IPO, kebabs, KEGGREST, LACE, MAGAR, magpie, mAPKL, massiR, MatrixQCvis, MatrixRider, MBttest, mCSEA, Mergeomics, Metab, MetaboSignal, metagene, metagene2, metagenomeSeq, MetCirc, methylCC, methylInheritance, MetNet, microbiome, microRNAome, MIGSAdata, miRBaseConverter, miRcomp, mirIntegrator, miRLAB, mnem, mosbi, motifStack, MsQuality, multiClust, MultiMed, multiOmicsViz, MultiRNAflow, MungeSumstats, MWASTools, ncRNAtools, nempi, netbiov, NetSAM, nondetects, NoRCE, nucleoSim, OMICsPCA, OncoScore, PAA, panelcn.mops, Path2PPI, PathNet, pathview, PCAtools, pepXMLTab, phenomis, PhenStat, powerTCR, proBAMr, pwrEWAS, pwrEWAS.data, qpgraph, quantro, QuartPAC, RBGL, rBiopaxParser, rcellminer, rCGH, REBET, RegParallel, RESOLVE, rfaRm, RGraph2js, Rgraphviz, rgsepd, riboSeqR, ROntoTools, ropls, ROSeq, RTN, RTNduals, RTNsurvival, rTRM, SAIGEgds, sangerseqR, SANTA, sarks, SCArray, scDataviz, scmeth, scMultiome, screenCounter, scry, segmentSeq, SeqArray, seqPattern, seqTools, sesameData, SICtools, sigFeature, sigsquared, SIMAT, similaRpeak, SIMLR, singleCellTK, SingleR, slingshot, SNPRelate, SpacePAC, sparseDOSSA, SparseSignatures, spatialHeatmap, specL, STATegRa, STRINGdb, SUITOR, systemPipeTools, TCC, TFEA.ChIP, TIN, transcriptogramer, traseR, TreeAndLeaf, trena, tripr, tRNAdbImport, TRONCO, Uniquorn, variancePartition, VERSO, xcore, xcoredata, zenith
Links To Me
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Package Archives

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

Source Package BiocGenerics_0.48.1.tar.gz
Windows Binary BiocGenerics_0.48.1.zip
macOS Binary (x86_64) BiocGenerics_0.48.1.tgz
macOS Binary (arm64) BiocGenerics_0.48.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocGenerics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocGenerics
Bioc Package Browser https://code.bioconductor.org/browse/BiocGenerics/
Package Short Url https://bioconductor.org/packages/BiocGenerics/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive