BiocGenerics

DOI: 10.18129/B9.bioc.BiocGenerics    

S4 generic functions used in Bioconductor

Bioconductor version: Release (3.13)

The package defines many S4 generic functions used in Bioconductor.

Author: The Bioconductor Dev Team

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("BiocGenerics")

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

Documentation

PDF   Reference Manual

Details

biocViews Infrastructure, Software
Version 0.38.0
In Bioconductor since BioC 2.10 (R-2.15) (9.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, utils, graphics, stats, parallel
Imports methods, utils, graphics, stats, parallel
LinkingTo
Suggests Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit
SystemRequirements
Enhances
URL https://bioconductor.org/packages/BiocGenerics
BugReports https://github.com/Bioconductor/BiocGenerics/issues
Depends On Me ACME, affy, affyPLM, altcdfenvs, amplican, AnnotationDbi, AnnotationForge, AnnotationHub, ATACseqQC, beadarray, bioassayR, Biobase, Biostrings, bnbc, BSgenome, bsseq, Cardinal, Category, categoryCompare, ChAMPdata, chipseq, ChIPseqR, ChromHeatMap, clusterExperiment, codelink, consensusDE, consensusSeekeR, copynumber, CoreGx, CRISPRseek, cummeRbund, DelayedArray, dexus, ensembldb, ensemblVEP, ExperimentHub, ExperimentHubData, GDSArray, geneplotter, GenomeInfoDb, genomeIntervals, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges, GenomicScores, genoset, ggbio, girafe, graph, GSEABase, GUIDEseq, HelloRanges, interactiveDisplay, interactiveDisplayBase, IRanges, liftOver, MBASED, MeSHDbi, methyAnalysis, MIGSA, MineICA, minfi, MLInterfaces, MotifDb, mpra, MSnbase, multtest, NADfinder, ngsReports, oligo, OrganismDbi, pandaR, plethy, plyranges, PoTRA, profileplyr, PSICQUIC, PWMEnrich, QSutils, RareVariantVis, REDseq, Repitools, RNAprobR, RnBeads, RPA, rsbml, S4Vectors, shinyMethyl, ShortRead, simplifyEnrichment, simulatorZ, soGGi, spqn, StructuralVariantAnnotation, SummarizedBenchmark, TEQC, tigre, topdownr, topGO, UNDO, UniProt.ws, VanillaICE, VariantAnnotation, VariantFiltering, VCFArray, XVector, yamss
Imports Me a4Preproc, affycoretools, affylmGUI, AllelicImbalance, AneuFinder, annmap, annotate, AnnotationHubData, ArrayExpressHTS, ASpli, AUCell, autonomics, bambu, bamsignals, BASiCS, batchelor, beachmat, bigmelon, biocGraph, BiocIO, BiocSingular, biotmle, biovizBase, biscuiteer, BiSeq, blima, breakpointR, BrowserViz, BSgenome, BubbleTree, bumphunter, BUSpaRse, CAGEfightR, CAGEr, casper, celaref, CellaRepertorium, CellBench, cellHTS2, CellMixS, CellTrails, cgdv17, cghMCR, ChemmineDrugs, ChemmineOB, ChemmineR, ChIC, ChIPComp, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPQC, ChIPseeker, chipseq, ChIPSeqSpike, chromstaR, chromVAR, cicero, clusterSeq, cn.mops, CNEr, CNVPanelizer, CNVRanger, COCOA, cola, compEpiTools, contiBAIT, crlmm, crossmeta, csaw, ctgGEM, cummeRbund, curatedCRCData, curatedOvarianData, cydar, dada2, dagLogo, DAMEfinder, ddCt, decompTumor2Sig, DEGreport, DelayedDataFrame, derfinder, DEScan2, DESeq2, destiny, DEWSeq, DEXSeq, diffcoexp, diffHic, DirichletMultinomial, DiscoRhythm, DRIMSeq, DropletUtils, DrugVsDisease, easyRNASeq, EBImage, EDASeq, eiR, eisa, eisaR, enrichTF, epialleleR, epigenomix, EpiTxDb, epivizrChart, epivizrStandalone, erma, esATAC, exomePeak2, ExpHunterSuite, FamAgg, fastseg, ffpe, FindMyFriends, flowBin, flowClust, flowCore, flowFP, FlowSOM, flowSpecs, flowStats, flowWorkspace, fmcsR, FRASER, frma, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, geneClassifiers, genefilter, GENESIS, GenomicAlignments, GenomicInteractions, GenomicTuples, genotypeeval, GenVisR, GeomxTools, glmGamPoi, gmapR, gmoviz, goseq, GOTHiC, gpuMagic, Gviz, HDF5Array, heatmaps, HiLDA, hiReadsProcessor, hopach, HTSeqGenie, icetea, igvR, IHW, IHWpaper, IMAS, infercnv, INSPEcT, InTAD, intansv, InteractionSet, IntEREst, IONiseR, iSEE, IsoformSwitchAnalyzeR, isomiRs, IVAS, KCsmart, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, ldblock, lisaClust, LOLA, maser, MAST, matter, MEAL, meshr, metaMS, metaseqR2, methInheritSim, MethylAid, methylPipe, methylumi, mia, miaViz, microbiomeDataSets, mimager, MinimumDistance, MIRA, MiRaGE, missMethyl, MMAPPR2, Modstrings, mogsa, monocle, motifbreakR, MouseGastrulationData, MouseThymusAgeing, msa, MSnID, MultiAssayExperiment, multicrispr, MultiDataSet, multiMiR, 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, podkat, pram, primirTSS, proDA, profileScoreDist, pRoloc, pRolocGUI, PureCN, pwOmics, QFeatures, qPLEXanalyzer, qsea, QuasR, R3CPET, R453Plus1Toolbox, RaggedExperiment, ramr, ramwas, RCAS, RcisTarget, RCy3, RCyjs, recoup, REMP, ReportingTools, RGalaxy, RGMQL, RGSEA, RiboProfiling, ribosomeProfilingQC, Ringo, RJMCMCNucleosomes, rnaEditr, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, roar, rols, Rqc, rqubic, Rsamtools, rsbml, rScudo, RTCGAToolbox, rtracklayer, SC3, SCArray, scater, scDblFinder, scmap, SCnorm, SCOPE, scPipe, scran, scRNAseq, scruff, scuttle, SeqVarTools, sevenC, SGSeq, SharedObject, signatureSearch, signeR, SingleCellExperiment, SingleCellMultiModal, SingleMoleculeFootprinting, sitadela, SLGI, SNPhood, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.GRCh38, snpStats, SpatialExperiment, Spectra, spicyR, splatter, SplicingGraphs, SQLDataFrame, sRACIPE, sscu, STAN, strandCheckR, Streamer, Structstrings, SummarizedExperiment, SynMut, systemPipeRdata, TAPseq, target, TarSeqQC, TBSignatureProfiler, TCGAutils, TCseq, TENxBUSData, TFBSTools, TitanCNA, trackViewer, transcriptR, transite, TransView, TreeSummarizedExperiment, tRNA, tRNAdbImport, tRNAscanImport, TSRchitect, TVTB, Ularcirc, UMI4Cats, unifiedWMWqPCR, universalmotif, uSORT, VariantTools, VariantToolsData, velociraptor, wavClusteR, weitrix, xcms, XDE, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector
Suggests Me acde, aggregateBioVar, AIMS, ASSET, BaalChIP, baySeq, BDMMAcorrect, bigmelon, bigmemoryExtras, bigPint, BiocCheck, BiocParallel, BiocStyle, biocViews, BioMM, biosigner, BiRewire, BLMA, BloodGen3Module, bnem, BUScorrect, CAFE, CAMERA, CancerSubtypes, CAnD, CausalR, ccrepe, cellmigRation, CellNOptR, CexoR, ChIPanalyser, ChIPXpress, CHRONOS, CINdex, cleanUpdTSeq, clipper, clonotypeR, clustComp, CNORfeeder, CNORfuzzy, coexnet, coMET, ConnectivityMap, consensus, cosmiq, COSNet, cpvSNP, CytoTree, DAPAR, DBChIP, DEsubs, DExMA, DMRcaller, DMRcate, ENCODExplorer, ENCODExplorerData, EnhancedVolcano, ENmix, epiNEM, EventPointer, fCCAC, fcScan, fgga, FGNet, FieldEffectCrc, flowCL, flowCut, FlowRepositoryR, flowTime, fmrs, GateFinder, gCrisprTools, gdsfmt, GEM, GeneNetworkBuilder, GeneOverlap, geneplast, geneRxCluster, geNetClassifier, genomation, GEOquery, GMRP, GOstats, GraphPAC, GreyListChIP, grndata, GSVA, GWASTools, h5vc, Harman, HarmanData, hiAnnotator, HiCDCPlus, hierGWAS, HIREewas, hypergraph, iCARE, iClusterPlus, illuminaio, immunotation, InPAS, INPower, IPO, kebabs, KEGGREST, LACE, LRBase.Ath.eg.db, LRBase.Bta.eg.db, LRBase.Cel.eg.db, LRBase.Dme.eg.db, LRBase.Dre.eg.db, LRBase.Gga.eg.db, LRBase.Hsa.eg.db, LRBase.Mmu.eg.db, LRBase.Pab.eg.db, LRBase.Rno.eg.db, LRBase.Ssc.eg.db, LRBase.Xtr.eg.db, LRBaseDbi, MAGAR, mAPKL, massiR, MatrixQCvis, MatrixRider, MBttest, mCSEA, mdgsa, Mergeomics, MeSH.Aca.eg.db, MeSH.Aga.PEST.eg.db, MeSH.Ame.eg.db, MeSH.Aml.eg.db, MeSH.Ana.eg.db, MeSH.Ani.FGSC.eg.db, MeSH.AOR.db, MeSH.Ath.eg.db, MeSH.Bfl.eg.db, MeSH.Bsu.168.eg.db, MeSH.Bta.eg.db, MeSH.Cal.SC5314.eg.db, MeSH.Cbr.eg.db, MeSH.Cel.eg.db, MeSH.Cfa.eg.db, MeSH.Cin.eg.db, MeSH.Cja.eg.db, MeSH.Cpo.eg.db, MeSH.Cre.eg.db, MeSH.Dan.eg.db, MeSH.db, MeSH.Dda.3937.eg.db, MeSH.Ddi.AX4.eg.db, MeSH.Der.eg.db, MeSH.Dgr.eg.db, MeSH.Dme.eg.db, MeSH.Dmo.eg.db, MeSH.Dpe.eg.db, MeSH.Dre.eg.db, MeSH.Dse.eg.db, MeSH.Dsi.eg.db, MeSH.Dvi.eg.db, MeSH.Dya.eg.db, MeSH.Eca.eg.db, MeSH.Eco.K12.MG1655.eg.db, MeSH.Eco.O157.H7.Sakai.eg.db, MeSH.Gga.eg.db, MeSH.Gma.eg.db, MeSH.Hsa.eg.db, MeSH.Laf.eg.db, MeSH.Lma.eg.db, MeSH.Mdo.eg.db, MeSH.Mes.eg.db, MeSH.Mga.eg.db, MeSH.Miy.eg.db, MeSH.Mml.eg.db, MeSH.Mmu.eg.db, MeSH.Mtr.eg.db, MeSH.Nle.eg.db, MeSH.Oan.eg.db, MeSH.Ocu.eg.db, MeSH.Oni.eg.db, MeSH.Osa.eg.db, MeSH.Pab.eg.db, MeSH.Pae.PAO1.eg.db, MeSH.PCR.db, MeSH.Pfa.3D7.eg.db, MeSH.Pto.eg.db, MeSH.Ptr.eg.db, MeSH.Rno.eg.db, MeSH.Sce.S288c.eg.db, MeSH.Sco.A32.eg.db, MeSH.Sil.eg.db, MeSH.Spu.eg.db, MeSH.Ssc.eg.db, MeSH.Syn.eg.db, MeSH.Tbr.9274.eg.db, MeSH.Tgo.ME49.eg.db, MeSH.Tgu.eg.db, MeSH.Vvi.eg.db, MeSH.Xla.eg.db, MeSH.Xtr.eg.db, MeSH.Zma.eg.db, Metab, MetaboSignal, metagene, metagene2, metagenomeSeq, MetCirc, methylCC, methylInheritance, MetNet, microbiome, microRNAome, MIGSAdata, miRBaseConverter, miRcomp, mirIntegrator, miRLAB, mnem, motifStack, MSEADbi, multiClust, MultiMed, multiOmicsViz, MungeSumstats, MWASTools, NBSplice, ncRNAtools, nempi, netbiov, NetSAM, nondetects, NoRCE, nucleoSim, OMICsPCA, OncoScore, PAA, panelcn.mops, Path2PPI, PathNet, pathview, PCAtools, pepXMLTab, PhenStat, powerTCR, proBAMr, proFIA, pwrEWAS, pwrEWAS.data, qpgraph, quantro, QuartPAC, RBGL, rBiopaxParser, Rcade, rcellminer, rCGH, Rcpi, REBET, RegParallel, rfaRm, RGraph2js, Rgraphviz, rgsepd, riboSeqR, ROntoTools, ropls, ROSeq, RTN, RTNduals, RTNsurvival, rTRM, SAIGEgds, samExploreR, sangerseqR, SANTA, sarks, scDataviz, scmeth, scry, segmentSeq, SeqArray, seqPattern, seqTools, sesameData, SICtools, sigFeature, sigsquared, SIMAT, similaRpeak, SIMLR, singleCellTK, SingleR, slingshot, SNPRelate, sojourner, SpacePAC, sparseDOSSA, SparseSignatures, spatialHeatmap, specL, STATegRa, STRINGdb, systemPipeR, systemPipeTools, TCC, TFEA.ChIP, TIN, transcriptogramer, TraRe, traseR, TreeAndLeaf, trena, TRONCO, Uniquorn, variancePartition, VERSO
Links To Me
Build Report  

Package Archives

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

Source Package BiocGenerics_0.38.0.tar.gz
Windows Binary BiocGenerics_0.38.0.zip
macOS 10.13 (High Sierra) BiocGenerics_0.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocGenerics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocGenerics
Package Short Url https://bioconductor.org/packages/BiocGenerics/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: