BiocGenerics

DOI: 10.18129/B9.bioc.BiocGenerics  

S4 generic functions used in Bioconductor

Bioconductor version: Release (3.16)

The package defines many S4 generic functions used in Bioconductor.

Author: The Bioconductor Dev Team

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

Installation

To install this package, start R (version "4.2") 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

PDF		Reference Manual

Details

biocViews	Infrastructure, Software
Version	0.44.0
In Bioconductor since	BioC 2.10 (R-2.15) (11 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, utils, graphics, stats
Imports	methods, utils, graphics, stats
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, 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, MIGSA, MineICA, minfi, MLInterfaces, MotifDb, mpra, MSnbase, multtest, NADfinder, ngsReports, oligo, OrganismDbi, pandaR, plethy, plyranges, PoTRA, profileplyr, PWMEnrich, QSutils, RareVariantVis, REDseq, Repitools, RnBeads, RPA, rsbml, S4Vectors, shinyMethyl, ShortRead, simplifyEnrichment, soGGi, spqn, StructuralVariantAnnotation, SummarizedBenchmark, svaNUMT, svaRetro, TEQC, tigre, topdownr, topGO, UNDO, UniProt.ws, updateObject, VanillaICE, VariantAnnotation, VariantFiltering, VCFArray, XVector, yamss
Imports Me	a4Preproc, affycoretools, affylmGUI, AllelicImbalance, AneuFinder, annmap, annotate, AnnotationHubData, ArrayExpressHTS, ASpli, ATACseqTFEA, atena, 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, cfDNAPro, cghMCR, ChemmineDrugs, ChemmineOB, ChemmineR, ChIC, 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, ctgGEM, cummeRbund, curatedCRCData, curatedOvarianData, cydar, dada2, dagLogo, DAMEfinder, ddCt, decompTumor2Sig, deconvR, DEGreport, DelayedDataFrame, derfinder, DEScan2, DESeq2, destiny, DEWSeq, DEXSeq, diffcoexp, diffHic, DirichletMultinomial, DiscoRhythm, 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, genbankr, geneAttribution, geneClassifiers, genefilter, GENESIS, GenomAutomorphism, GenomicAlignments, GenomicInteractions, GenomicTuples, genotypeeval, GenVisR, GeomxTools, GeoMxWorkflows, glmGamPoi, gmapR, gmoviz, goseq, GOTHiC, gpuMagic, Gviz, HDF5Array, heatmaps, hermes, HiCDOC, 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, LinTInd, lisaClust, LOLA, 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, MSnID, MultiAssayExperiment, multicrispr, MultiDataSet, multiMiR, mumosa, MutationalPatterns, mzR, NanoStringNCTools, ncdfFlow, nearBynding, npGSEA, nucleR, NxtIRFcore, ODER, 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, ProteoDisco, PSMatch, PureCN, pwOmics, QFeatures, qPLEXanalyzer, qsea, QuasR, R3CPET, R453Plus1Toolbox, RadioGx, 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, scater, scDblFinder, scmap, SCnorm, SCOPE, scPipe, scran, scRNAseq, scruff, scuttle, SeqVarTools, sevenC, SGSeq, SharedObject, signatureSearch, signeR, signifinder, single, SingleCellExperiment, SingleCellMultiModal, 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, STAN, standR, strandCheckR, Streamer, Structstrings, SummarizedExperiment, SynMut, systemPipeR, systemPipeRdata, TAPseq, target, TarSeqQC, TBSignatureProfiler, TCGAutils, TCseq, TENxBUSData, TENxIO, TFBSTools, TitanCNA, ToxicoGx, trackViewer, transcriptR, transite, TransView, TreeSummarizedExperiment, tRNA, tRNAdbImport, 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, 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, cellmigRation, CellNOptR, CexoR, ChIPanalyser, ChIPXpress, CHRONOS, CINdex, cleanUpdTSeq, clipper, clustComp, CNORfeeder, CNORfuzzy, coexnet, coMET, ConnectivityMap, consensus, cosmiq, COSNet, cpvSNP, CytoTree, DEsubs, DExMA, DMRcaller, DMRcate, ENCODExplorerData, EnhancedVolcano, ENmix, EpiMix, epiNEM, EventPointer, fCCAC, fcScan, fgga, FGNet, FieldEffectCrc, flowCL, flowCut, flowTime, fmrs, GateFinder, gCrisprTools, gdsfmt, GEM, GeneNetworkBuilder, GeneOverlap, geneplast, geneplast.data, geneRxCluster, geNetClassifier, genomation, GEOquery, GMRP, GOstats, GraphPAC, GreyListChIP, grndata, GSVA, GWASTools, h5vc, Harman, HarmanData, healthyControlsPresenceChecker, hiAnnotator, HiCDCPlus, hierGWAS, HIREewas, HPiP, hypergraph, iCARE, iClusterPlus, illuminaio, immunotation, InPAS, INPower, IPO, kebabs, KEGGREST, LACE, MAGAR, 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, multiClust, MultiMed, multiOmicsViz, MungeSumstats, MWASTools, NBSplice, ncRNAtools, nempi, netbiov, NetSAM, nondetects, NoRCE, nucleoSim, OMICsPCA, OncoScore, PAA, panelcn.mops, Path2PPI, PathNet, pathview, PCAtools, pepXMLTab, phenomis, PhenStat, powerTCR, proBAMr, proFIA, pwrEWAS, pwrEWAS.data, qpgraph, quantro, QuartPAC, RBGL, rBiopaxParser, Rcade, rcellminer, rCGH, Rcpi, REBET, RegParallel, RESOLVE, rfaRm, RGraph2js, Rgraphviz, rgsepd, riboSeqR, ROntoTools, ropls, ROSeq, RTN, RTNduals, RTNsurvival, rTRM, SAIGEgds, 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, SUITOR, systemPipeTools, TCC, TFEA.ChIP, TIN, transcriptogramer, TraRe, traseR, TreeAndLeaf, trena, tripr, TRONCO, Uniquorn, variancePartition, VERSO, xcore, xcoredata, zenith
Links To Me
Build Report

Package Archives

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

Source Package	BiocGenerics_0.44.0.tar.gz
Windows Binary	BiocGenerics_0.44.0.zip
macOS Binary (x86_64)	BiocGenerics_0.44.0.tgz
macOS Binary (arm64)	BiocGenerics_0.44.0.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