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S4Vectors

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see S4Vectors.

Foundation of vector-like and list-like containers in Bioconductor


Bioconductor version: 3.19

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Author: Hervé Pagès [aut, cre], Michael Lawrence [aut], Patrick Aboyoun [aut], Aaron Lun [ctb], Beryl Kanali [ctb] (Converted vignettes from Sweave to RMarkdown)

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

Citation (from within R, enter citation("S4Vectors")):

Installation

To install this package, start R (version "4.4") and enter: 


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

BiocManager::install("S4Vectors")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("S4Vectors")
A quick overview of the S4 class system PDF R Script
An Overview of the S4Vectors package HTML R Script
Rle Tips and Tricks HTML R Script
Reference Manual PDF
NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Infrastructure, Software
Version 0.42.1
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics(>= 0.37.0)
Imports
System Requirements
URL https://bioconductor.org/packages/S4Vectors
Bug Reports https://github.com/Bioconductor/S4Vectors/issues
See More
Suggests IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr
Linking To
Enhances
Depends On Me ATACseqQC, AnnotationHubData, BSgenome, BiSeq, Biostrings, CODEX, CSAR, CSSQ, Cardinal, CellMapper, CexoR, ChIPpeakAnno, ChIPseqR, ClassifyR, CompoundDb, DESeq2, DEXSeq, DMCFB, DMCHMM, DMRcaller, DelayedArray, DelayedDataFrame, DirichletMultinomial, ExperimentHubData, ExpressionAtlas, GA4GHclient, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicScores, GenomicTuples, GeomxTools, Gviz, HERON, HelloRanges, IRanges, InTAD, IntEREst, LinTInd, LoomExperiment, MSnbase, MetNet, MotifDb, MuData, MultimodalExperiment, NADfinder, NBAMSeq, NanoStringNCTools, OGRE, OTUbase, PSMatch, RNAmodR, Rcwl, RegEnrich, RepViz, RnBeads, S4Arrays, SQLDataFrame, SeqGate, SparseArray, Spectra, Structstrings, TRESS, TreeSummarizedExperiment, VariantExperiment, VariantTools, XVector, altcdfenvs, bambu, bandle, betaHMM, bumphunter, chimeraviz, chipseq, cliProfiler, coseq, epigenomix, fCCAC, girafe, groHMM, hdxmsqc, m6Aboost, octad, padma, pwalign, scDataviz, screenCounter, segmentSeq, seqArchRplus, topdownr, triplex, txdbmaker, updateObject, vulcan, pd.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.ath1.121501, pd.barley1, pd.bovgene.1.0.st, pd.bovgene.1.1.st, pd.bovine, pd.bsubtilis, pd.cangene.1.0.st, pd.cangene.1.1.st, pd.canine, pd.canine.2, pd.celegans, pd.chicken, pd.chigene.1.0.st, pd.chigene.1.1.st, pd.chogene.2.0.st, pd.chogene.2.1.st, pd.citrus, pd.clariom.d.human, pd.clariom.s.human, pd.clariom.s.human.ht, pd.clariom.s.mouse, pd.clariom.s.mouse.ht, pd.clariom.s.rat, pd.clariom.s.rat.ht, pd.cotton, pd.cyngene.1.0.st, pd.cyngene.1.1.st, pd.cyrgene.1.0.st, pd.cyrgene.1.1.st, pd.cytogenetics.array, pd.drogene.1.0.st, pd.drogene.1.1.st, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.elegene.1.0.st, pd.elegene.1.1.st, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.fingene.1.0.st, pd.fingene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.guigene.1.0.st, pd.guigene.1.1.st, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.hg18.60mer.expr, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hta.2.0, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.hugene.2.0.st, pd.hugene.2.1.st, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.margene.1.0.st, pd.margene.1.1.st, pd.medgene.1.0.st, pd.medgene.1.1.st, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.4.0, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177, pd.ovigene.1.0.st, pd.ovigene.1.1.st, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.porgene.1.0.st, pd.porgene.1.1.st, pd.rabgene.1.0.st, pd.rabgene.1.1.st, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.ragene.2.0.st, pd.ragene.2.1.st, pd.rat230.2, pd.rcngene.1.0.st, pd.rcngene.1.1.st, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhegene.1.0.st, pd.rhegene.1.1.st, pd.rhesus, pd.rice, pd.rjpgene.1.0.st, pd.rjpgene.1.1.st, pd.rn.u34, pd.rta.1.0, pd.rusgene.1.0.st, pd.rusgene.1.1.st, pd.s.aureus, pd.soybean, pd.soygene.1.0.st, pd.soygene.1.1.st, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebgene.1.0.st, pd.zebgene.1.1.st, pd.zebrafish, curatedPCaData, scATAC.Explorer, generegulation
Imports Me ADImpute, ALDEx2, ANCOMBC, ASURAT, ASpli, ATACseqTFEA, AllelicImbalance, AneuFinder, AnnotationDbi, AnnotationForge, AnnotationHub, BASiCS, BPRMeth, BREW3R.r, BSgenomeForge, BUSpaRse, BUSseq, BadRegionFinder, Banksy, BayesSpace, BiSeq, BindingSiteFinder, BiocHubsShiny, BiocIO, BiocNeighbors, BiocOncoTK, BiocSet, BiocSingular, BumpyMatrix, CAGEfightR, CAGEr, CATALYST, CHETAH, CNEr, CNVMetrics, CNVPanelizer, CNVRanger, COCOA, CRISPRseek, CTDquerier, CardinalIO, CeTF, CellBarcode, Cepo, ChIPQC, ChIPexoQual, ChIPseeker, ChromSCape, CircSeqAlignTk, CiteFuse, CluMSID, CoGAPS, Cogito, CoreGx, CoverageView, CrispRVariants, CuratedAtlasQueryR, DAMEfinder, DECIPHER, DEFormats, DEGreport, DEScan2, DESpace, DEWSeq, DMRcate, DNAfusion, DRIMSeq, DegCre, DegNorm, DelayedMatrixStats, DiffBind, Dino, DiscoRhythm, DropletUtils, ELMER, EnrichmentBrowser, EpiMix, EpiTxDb, EventPointer, ExperimentHub, ExperimentSubset, ExploreModelMatrix, FLAMES, FRASER, FastqCleaner, FilterFFPE, FindIT2, FuseSOM, GA4GHshiny, GDSArray, GENESIS, GOTHiC, GOpro, GRaNIE, GRmetrics, GSEABenchmarkeR, GSVA, GUIDEseq, GeneRegionScan, GeneTonic, GenomAutomorphism, GenomicAlignments, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicSuperSignature, Glimma, HDF5Array, HTSeqGenie, HiCBricks, HiCDOC, HiCExperiment, HiCcompare, HiContacts, HiCool, HiLDA, HicAggR, HumanTranscriptomeCompendium, IFAA, ILoReg, IMAS, INSPEcT, IVAS, InterMineR, InteractionSet, InteractiveComplexHeatmap, IsoBayes, IsoformSwitchAnalyzeR, LOLA, MACSr, MADSEQ, MAI, MAST, MEAL, MGnifyR, MICSQTL, MIRA, MMDiff2, MOSim, MSPrep, MesKit, MetCirc, MetaboAnnotation, MethReg, MiRaGE, MinimumDistance, Modstrings, MoleculeExperiment, Motif2Site, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MsCoreUtils, MsExperiment, MultiAssayExperiment, MultiDataSet, MultiRNAflow, MutationalPatterns, NanoMethViz, ORFik, OUTRIDER, Organism.dplyr, OrganismDbi, OutSplice, PAIRADISE, PAST, PDATK, PING, PWMEnrich, Pedixplorer, PhIPData, PharmacoGx, PhosR, ProteoDisco, PureCN, QFeatures, QTLExperiment, QuasR, R3CPET, R453Plus1Toolbox, RAIDS, RBioFormats, RCAS, REMP, RESOLVE, RGMQL, RJMCMCNucleosomes, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RTCGAToolbox, RTN, RadioGx, RaggedExperiment, RareVariantVis, RcisTarget, RcwlPipelines, ReUseData, RegionalST, Repitools, ResidualMatrix, RgnTX, RiboDiPA, RiboProfiling, Rmmquant, Rqc, Rsamtools, SC3, SCArray.sat, SCArray, SCOPE, SCnorm, SEtools, SGSeq, SMITE, SNPhood, SOMNiBUS, SPLINTER, ScaledMatrix, SeqArray, SeqSQC, SeqVarTools, ShortRead, SingleCellAlleleExperiment, SingleCellExperiment, SingleR, SomaticSignatures, Spaniel, SpatialExperiment, SpatialFeatureExperiment, SpatialOmicsOverlay, SpliceWiz, SplicingGraphs, SpotClean, Statial, StructuralVariantAnnotation, SummarizedExperiment, SynExtend, TAPseq, TBSignatureProfiler, TCGAbiolinks, TCGAutils, TENxIO, TFBSTools, TFHAZ, TSCAN, TVTB, TileDBArray, TnT, ToxicoGx, TrajectoryUtils, TransView, Trendy, UCSC.utils, UMI4Cats, UPDhmm, Ularcirc, VCFArray, VDJdive, VaSP, VanillaICE, VariantAnnotation, VariantFiltering, VisiumIO, Voyager, VplotR, XNAString, XVector, adverSCarial, affycoretools, aggregateBioVar, airpart, alabaster.base, alabaster.bumpy, alabaster.files, alabaster.mae, alabaster.matrix, alabaster.ranges, alabaster.se, alabaster.spatial, alabaster.string, alabaster.vcf, amplican, animalcules, annotatr, appreci8R, atena, autonomics, ballgown, barcodetrackR, batchelor, bettr, biotmle, biovizBase, biscuiteer, bluster, bnbc, branchpointer, breakpointR, bsseq, cBioPortalData, cardelino, casper, ccfindR, celaref, celda, censcyt, cfdnakit, chipenrich, chromVAR, chromstaR, cicero, circRNAprofiler, cleanUpdTSeq, cleaver, clusterExperiment, clustifyr, cn.mops, comapr, compEpiTools, consensusDE, consensusSeekeR, crisprBase, crisprDesign, crisprShiny, crisprViz, csaw, cummeRbund, customProDB, cydar, cytoKernel, cytofQC, cytomapper, cytoviewer, dStruct, debrowser, decompTumor2Sig, decontX, deconvR, derfinderHelper, derfinderPlot, derfinder, diffHic, diffUTR, diffcyt, dittoSeq, dmrseq, doseR, dreamlet, drugTargetInteractions, easyRNASeq, eisaR, enhancerHomologSearch, ensemblVEP, ensembldb, epigraHMM, epimutacions, epiregulon, epistack, epivizrData, epivizrStandalone, epivizr, erma, esATAC, extraChIPs, factR, fastseg, fishpond, flowCore, flowWorkspace, gDNAx, gDRcore, gDRimport, gDRutils, gcapc, gemma.R, genomation, genomeIntervals, ggbio, gmapR, gmoviz, gwascat, h5vc, hermes, hicVennDiagram, hipathia, hmdbQuery, iSEE, iSEEde, iSEEhub, iSEEpathways, iSEEu, icetea, ideal, imcRtools, isomiRs, ivygapSE, karyoploteR, katdetectr, kebabs, knowYourCG, lefser, lemur, limpca, lionessR, lipidr, lisaClust, loci2path, lute, mCSEA, magpie, mariner, marr, mbkmeans, meshr, metabCombiner, metaseqR2, methInheritSim, methodical, methrix, methylCC, methylInheritance, methylKit, methylPipe, methylSig, methylumi, miaSim, miaViz, mia, microbiomeMarker, midasHLA, miloR, mimager, minfi, missMethyl, missRows, mitoClone2, moanin, mobileRNA, monaLisa, mosaics, mosdef, motifTestR, motifbreakR, motifmatchr, mpra, msa, msgbsR, multistateQTL, mumosa, muscat, musicatk, mygene, myvariant, ncRNAtools, nearBynding, nucleR, nucleoSim, nullranges, oligoClasses, omicsViewer, oncoscanR, ontoProc, openPrimeR, orthos, packFinder, pairedGSEA, panelcn.mops, pcaExplorer, pdInfoBuilder, periodicDNA, pgxRpi, pipeComp, plyinteractions, plyranges, pmp, pogos, polyester, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, proDA, procoil, profileplyr, qcmetrics, qpgraph, qsea, rGREAT, rScudo, raer, ramr, recount3, recount, recountmethylation, recoup, regionReport, regioneR, regsplice, regutools, rexposome, rfaRm, riboSeqR, ribor, ribosomeProfilingQC, rifiComparative, rifi, rnaEditr, roar, rprimer, rtracklayer, sRACIPE, saseR, scClassify, scDD, scDblFinder, scHOT, scMET, scMerge, scPipe, scRNAseqApp, scRepertoire, scTGIF, scTensor, scTreeViz, scanMiRApp, scanMiR, scater, scds, scider, scmap, scp, scran, scruff, scuttle, scviR, sechm, segmenter, seqCAT, seqsetvis, sesame, sevenC, sevenbridges, simPIC, simona, simpleSeg, singleCellTK, singscore, sitadela, skewr, slingshot, soGGi, spatialHeatmap, spatzie, spicyR, spiky, spillR, splatter, srnadiff, standR, strandCheckR, struct, svaNUMT, svaRetro, systemPipeR, tRNA, tRNAdbImport, tRNAscanImport, tadar, terraTCGAdata, tidyCoverage, tidySingleCellExperiment, tidySpatialExperiment, tidySummarizedExperiment, tidybulk, trackViewer, tradeSeq, transcriptR, transmogR, treeclimbR, tricycle, twoddpcr, txcutr, tximeta, universalmotif, velociraptor, wavClusteR, weitrix, wiggleplotr, xcms, xcore, yamss, zellkonverter, BioMartGOGeneSets, fitCons.UCSC.hg19, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.v3.1.2.GRCh38, MafH5.gnomAD.v4.0.GRCh38, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, 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, celldex, chipenrich.data, chipseqDBData, curatedMetagenomicData, curatedTCGAData, DNAZooData, DropletTestFiles, FlowSorted.Blood.EPIC, fourDNData, HCATonsilData, HighlyReplicatedRNASeq, HMP16SData, HMP2Data, homosapienDEE2CellScore, imcdatasets, leeBamViews, MerfishData, MetaGxPancreas, MetaScope, MethylSeqData, MicrobiomeBenchmarkData, MouseGastrulationData, MouseThymusAgeing, pd.atdschip.tiling, scMultiome, scpdata, scRNAseq, sesameData, SimBenchData, SingleCellMultiModal, SomaticCancerAlterations, spatialLIBD, TransOmicsData, tuberculosis, GeoMxWorkflows, seqpac, crispRdesignR, DR.SC, driveR, genBaRcode, geno2proteo, hoardeR, imcExperiment, karyotapR, LoopRig, MetAlyzer, microbial, MOCHA, multimedia, NIPTeR, oncoPredict, PlasmaMutationDetector, PlasmaMutationDetector2, restfulr, rliger, rnaCrosslinkOO, rsolr, SC.MEB, SCRIP, scROSHI, Signac, SpatialDDLS, TaxaNorm, toxpiR
Suggests Me AlpsNMR, BiocGenerics, GWASTools, GWENA, GeoTcgaData, MicrobiotaProcess, MsQuality, MungeSumstats, RTCGA, SPOTlight, TFEA.ChIP, TFutils, chihaya, dearseq, epiregulon.extra, epivizrChart, globalSeq, gypsum, hca, maftools, martini, scFeatures, traviz, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, BioPlex, curatedAdipoChIP, curatedAdipoRNA, ObMiTi, xcoredata, gkmSVM, grandR, LorMe, MARVEL, pmartR, polyRAD, Rgff, Seurat, SNPassoc, updog, valr
Links To Me Biostrings, CNEr, DECIPHER, DelayedArray, GenomicAlignments, GenomicRanges, HDF5Array, IRanges, MatrixRider, Rsamtools, S4Arrays, ShortRead, SparseArray, Structstrings, VariantAnnotation, VariantFiltering, XVector, kebabs, pwalign, rtracklayer, triplex
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Package Archives

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

Source Package S4Vectors_0.42.1.tar.gz
Windows Binary (x86_64) S4Vectors_0.42.1.zip (64-bit only)
macOS Binary (x86_64) S4Vectors_0.42.1.tgz
macOS Binary (arm64) S4Vectors_0.42.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/S4Vectors
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/S4Vectors
Bioc Package Browser https://code.bioconductor.org/browse/S4Vectors/
Package Short Url https://bioconductor.org/packages/S4Vectors/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive