BiocGenerics

DOI: 10.18129/B9.bioc.BiocGenerics    

S4 generic functions used in Bioconductor

Bioconductor version: Release (3.14)

The package defines many S4 generic functions used in Bioconductor.

Author: The Bioconductor Dev Team

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

Installation

To install this package, start R (version "4.1") 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	0.40.0
In Bioconductor since	BioC 2.10 (R-2.15) (10 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, liftOver, MBASED, MIGSA, MineICA, minfi, MLInterfaces, MotifDb, mpra, MSnbase, multtest, NADfinder, ngsReports, oligo, OrganismDbi, pandaR, plethy, plyranges, PoTRA, profileplyr, PSICQUIC, 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, VanillaICE, VariantAnnotation, VariantFiltering, VCFArray, XVector, yamss
Imports Me	a4Preproc, affycoretools, affylmGUI, AllelicImbalance, AneuFinder, annmap, annotate, AnnotationHubData, ArrayExpressHTS, ASpli, 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, cghMCR, ChemmineDrugs, ChemmineOB, ChemmineR, ChIC, ChIPComp, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPQC, ChIPseeker, chipseq, 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, deconvR, DEGreport, DelayedDataFrame, derfinder, DEScan2, DESeq2, destiny, DEWSeq, DEXSeq, diffcoexp, diffHic, DirichletMultinomial, DiscoRhythm, DRIMSeq, DropletUtils, DrugVsDisease, easyRNASeq, EBImage, EDASeq, eiR, eisaR, enhancerHomologSearch, enrichTF, epialleleR, epigenomix, epistack, EpiTxDb, epivizrChart, epivizrStandalone, erma, esATAC, exomePeak2, ExpHunterSuite, FamAgg, fastseg, ffpe, FindIT2, 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, GeoMxWorkflows, 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, microbiomeMarker, mimager, MinimumDistance, MIRA, MiRaGE, missMethyl, MMAPPR2, Modstrings, mogsa, monaLisa, monocle, 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, PureCN, pwOmics, QFeatures, qPLEXanalyzer, qsea, QuasR, R3CPET, R453Plus1Toolbox, RaggedExperiment, ramr, ramwas, RCAS, RcisTarget, RCy3, RCyjs, recoup, REMP, ReportingTools, RGalaxy, RGMQL, RGSEA, RiboCrypt, 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, sparrow, SpatialExperiment, spatialLIBD, spatzie, Spectra, spicyR, splatter, SplicingGraphs, SQLDataFrame, sRACIPE, sscu, STAN, strandCheckR, Streamer, Structstrings, SummarizedExperiment, SynMut, systemPipeR, systemPipeRdata, TAPseq, target, TarSeqQC, TBSignatureProfiler, TCGAutils, TCseq, TENxBUSData, TFBSTools, TitanCNA, trackViewer, transcriptR, transite, TransView, TreeSummarizedExperiment, tRNA, tRNAdbImport, tRNAscanImport, TSRchitect, 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, BaalChIP, baySeq, BDMMAcorrect, bigmelon, bigPint, BiocCheck, BiocParallel, BiocStyle, biocViews, BioMM, biosigner, BiRewire, BLMA, BloodGen3Module, bnem, BUScorrect, BUSseq, 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, DEsubs, DExMA, DMRcaller, DMRcate, ENCODExplorer, ENCODExplorerData, EnhancedVolcano, ENmix, 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, 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, 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, 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, systemPipeTools, TCC, TFEA.ChIP, TIN, transcriptogramer, TraRe, traseR, TreeAndLeaf, trena, tripr, 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_0.40.0.tar.gz
Windows Binary	BiocGenerics_0.40.0.zip
macOS 10.13 (High Sierra)	BiocGenerics_0.40.0.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
Old Source Packages for BioC 3.14	Source Archive