This is the released version of BiocGenerics; for the devel version, see BiocGenerics.
S4 generic functions used in BioconductorBioconductor version: Release (3.21)
The package defines many S4 generic functions used in Bioconductor.
Author: The Bioconductor Dev Team [aut], Hervé Pagès [aut, cre] ORCID: 0009-0002-8272-4522 , Laurent Gatto [ctb] ORCID: 0000-0002-1520-2268 , Nathaniel Hayden [ctb], James Hester [ctb], Wolfgang Huber [ctb], Michael Lawrence [ctb], Martin Morgan [ctb] ORCID: 0000-0002-5874-8148 , Valerie Obenchain [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
Citation (from within R, entercitation("BiocGenerics")): Installation
To install this package, start R (version "4.5") 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 Details See More Suggests Biobase, S4Vectors, IRanges, S4Arrays, SparseArray, DelayedArray, HDF5Array, GenomicRanges, pwalign, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, MultiAssayExperiment, 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, chipseq, ChIPseqR, ChromHeatMap, clusterExperiment, codelink, consensusDE, consensusSeekeR, CoreGx, CRISPRseek, cummeRbund, DelayedArray, ensembldb, ExperimentHub, ExperimentHubData, GDSArray, geneplotter, GenomeInfoDb, genomeIntervals, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges, GenomicScores, ggbio, girafe, graph, GSEABase, GUIDEseq, h5mread, HelloRanges, interactiveDisplay, interactiveDisplayBase, IRanges, ISLET, lute, MBASED, MGnifyR, MineICA, minfi, MLInterfaces, MotifDb, mpra, MSnbase, multtest, NADfinder, ngsReports, oligo, OrganismDbi, plyranges, profileplyr, pwalign, PWMEnrich, QSutils, RareVariantVis, Rarr, REDseq, Repitools, RnBeads, RPA, rsbml, S4Arrays, S4Vectors, ShortRead, soGGi, SparseArray, spqn, StructuralVariantAnnotation, svaNUMT, svaRetro, TEQC, tigre, topdownr, topGO, txdbmaker, UNDO, updateObject, VanillaICE, VariantAnnotation, VariantFiltering, VCFArray, XVector, yamss, ChAMPdata, liftOver, rsolr 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, CellBench, CellMixS, CellTrails, cfDNAPro, cghMCR, ChemmineOB, ChemmineR, chipenrich, ChIPpeakAnno, ChIPQC, ChIPseeker, chipseq, chromVAR, cicero, CircSeqAlignTk, CleanUpRNAseq, clusterSeq, cn.mops, CNEr, CNVPanelizer, CNVRanger, COCOA, cola, compEpiTools, CompoundDb, concordexR, crisprBase, crisprBowtie, crisprBwa, crisprDesign, crisprScore, crisprShiny, crisprViz, crlmm, csaw, CTexploreR, cummeRbund, CuratedAtlasQueryR, cydar, dada2, dagLogo, DAMEfinder, dandelionR, ddCt, decompTumor2Sig, deconvR, DegCre, DEGreport, DelayedDataFrame, demuxSNP, derfinder, DEScan2, DESeq2, DESpace, destiny, DEWSeq, DEXSeq, DFplyr, diffcoexp, diffHic, dinoR, DirichletMultinomial, DiscoRhythm, DNAfusion, dreamlet, DRIMSeq, DropletUtils, DrugVsDisease, easyRNASeq, EBImage, EDASeq, eiR, eisaR, ELViS, enhancerHomologSearch, EnrichDO, epialleleR, EpiCompare, epigenomix, epimutacions, epistack, EpiTxDb, epivizrChart, epivizrStandalone, erma, esATAC, factR, FamAgg, fastseg, ffpe, FindIT2, FLAMES, flowBin, flowClust, flowCore, flowFP, FlowSOM, flowSpecs, flowStats, flowWorkspace, fmcsR, FRASER, frma, GA4GHclient, GA4GHshiny, gcapc, gDNAx, geneAttribution, geneClassifiers, GENESIS, GenomAutomorphism, GenomicAlignments, GenomicInteractions, GenomicPlot, GenomicTuples, GenVisR, geomeTriD, GeomxTools, gINTomics, glmGamPoi, gmapR, gmoviz, goseq, GOTHiC, gpuMagic, Gviz, HDF5Array, heatmaps, hermes, HicAggR, HiCDOC, HiCExperiment, HiContacts, HiCParser, HiLDA, hiReadsProcessor, hopach, icetea, igvR, igvShiny, IHW, IMAS, infercnv, INSPEcT, intansv, InteractionSet, IntEREst, IONiseR, iSEE, IsoformSwitchAnalyzeR, isomiRs, IVAS, KCsmart, ldblock, lefser, lemur, LinTInd, lisaClust, LOLA, maaslin3, mariner, maser, MAST, matter, MEAL, meshr, MetaboAnnotation, metaMS, metaseqR2, methInheritSim, MethylAid, methylPipe, methylumi, mia, miaViz, miloR, mimager, MinimumDistance, MIRA, MiRaGE, missMethyl, mist, mobileRNA, Modstrings, mogsa, monaLisa, monocle, Moonlight2R, Motif2Site, motifbreakR, msa, MsBackendSql, MsExperiment, MSnID, MultiAssayExperiment, multicrispr, MultiDataSet, multiMiR, MultimodalExperiment, mumosa, MutationalPatterns, mzR, NanoStringNCTools, nearBynding, npGSEA, nucleR, oligoClasses, openCyto, openPrimeR, ORFik, OUTRIDER, parglms, pcaMethods, PDATK, pdInfoBuilder, PharmacoGx, PhIPData, PhosR, phyloseq, piano, PING, PIPETS, plyinteractions, podkat, pram, primirTSS, proDA, profileScoreDist, pRoloc, pRolocGUI, ProteoDisco, PSMatch, PureCN, QFeatures, qPLEXanalyzer, qsea, QTLExperiment, QuasR, R3CPET, R453Plus1Toolbox, RadioGx, raer, RaggedExperiment, ramr, ramwas, RCAS, RcisTarget, RCy3, RCyjs, recoup, ReducedExperiment, REMP, ReportingTools, RGSEA, RiboCrypt, RiboDiPA, RiboProfiling, ribosomeProfilingQC, RJMCMCNucleosomes, rnaEditr, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAseqCovarImpute, roar, rols, Rqc, rqubic, Rsamtools, rsbml, rScudo, RTCGAToolbox, rtracklayer, saseR, SC3, SCArray.sat, scater, scDblFinder, scDotPlot, scmap, SCnorm, SCOPE, scPipe, scran, scruff, scuttle, SeqVarTools, sevenC, SGSeq, SharedObject, shinyDSP, shinyMethyl, signatureSearch, signeR, signifinder, simPIC, SingleCellExperiment, SingleMoleculeFootprinting, sitadela, Site2Target, SNPhood, snpStats, sparrow, SpatialExperiment, SpatialFeatureExperiment, spatzie, Spectra, splatter, SpliceWiz, SplicingGraphs, SplineDV, SQLDataFrame, sRACIPE, sscu, StabMap, standR, strandCheckR, Streamer, Structstrings, SummarizedExperiment, SVP, SynMut, systemPipeR, tadar, TAPseq, target, TCGAutils, TCseq, TENxIO, TFBSTools, tidySpatialExperiment, TitanCNA, ToxicoGx, trackViewer, transcriptR, transite, TreeSummarizedExperiment, tRNA, tRNAscanImport, TVTB, txcutr, Ularcirc, UMI4Cats, unifiedWMWqPCR, UniProt.ws, universalmotif, uSORT, VariantTools, velociraptor, VisiumIO, visiumStitched, wavClusteR, weitrix, xcms, XDE, XeniumIO, XVector, zitools, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, chipenrich.data, curatedOvarianData, gDNAinRNAseqData, homosapienDEE2CellScore, IHWpaper, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, microbiomeDataSets, MouseGastrulationData, MouseThymusAgeing, raerdata, scRNAseq, spatialLIBD, systemPipeRdata, TENxBUSData, VariantToolsData, ExpHunterSuite, GeoMxWorkflows, crispRdesignR, DCLEAR, decompDL, EEMDlstm, geno2proteo, HiCociety, inDAGO, locuszoomr, oncoPredict, pathwayTMB, RNAseqQC, RobLoxBioC, SCRIP, Signac, TaxaNorm, toxpiR, treediff, TSdeeplearning Suggests Me acde, adverSCarial, aggregateBioVar, AIMS, AlphaMissenseR, ASSET, ASURAT, BaalChIP, baySeq, bigmelon, BiocParallel, BiocStyle, biocViews, biosigner, BiRewire, BLMA, BloodGen3Module, bnem, borealis, BUScorrect, BUSseq, CAFE, CAMERA, CausalR, ccrepe, CDI, cellmigRation, CexoR, chihaya, ChIPanalyser, ChIPXpress, CHRONOS, CINdex, cleanUpdTSeq, clipper, ClustAll, clustComp, CNORfeeder, CNORfuzzy, consensus, cosmiq, COSNet, cpvSNP, crumblr, cypress, DEsubs, DExMA, DMRcaller, DMRcate, DNAcycP2, EnhancedVolcano, ENmix, EpiMix, epiNEM, EventPointer, fCCAC, fcScan, fgga, FGNet, flowCut, flowTime, fmrs, GateFinder, gCrisprTools, gdsfmt, GEM, GeneNetworkBuilder, GeneOverlap, geneplast, geneRxCluster, geNetClassifier, genomation, GEOquery, GeoTcgaData, ginmappeR, GMRP, GOstats, GrafGen, GreyListChIP, GSVA, GWASTools, h5vc, Harman, hiAnnotator, HiCDCPlus, hierGWAS, HIREewas, HPiP, hypergraph, iCARE, iClusterPlus, IFAA, illuminaio, immunotation, INPower, IPO, kebabs, KEGGREST, LACE, MAGAR, magpie, massiR, MatrixQCvis, MatrixRider, MBttest, mCSEA, Mergeomics, MetaboSignal, metagene2, metagenomeSeq, MetCirc, methylCC, methylInheritance, MetNet, microbiome, miRBaseConverter, miRcomp, mirIntegrator, mnem, mosbi, MOSClip, motifStack, MsQuality, multiClust, MultiMed, MultiRNAflow, MungeSumstats, MWASTools, ncRNAtools, nempi, 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