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S4Vectors

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see S4Vectors.

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


Bioconductor version: 3.12

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, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Author: H. Pagès, M. Lawrence and P. Aboyoun

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

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

Installation

To install this package, start R (version "4.0") 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 PDF R Script
Rle Tips and Tricks PDF R Script
Reference Manual PDF
NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Infrastructure, Software
Version 0.28.1
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics(>= 0.36.0)
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
Linking To
Enhances
Depends On Me altcdfenvs, AnnotationHubData, ATACseqQC, bambu, Biostrings, BiSeq, BRGenomics, BSgenome, bumphunter, Cardinal, CellMapper, CexoR, chimeraviz, ChIPComp, ChIPpeakAnno, chipseq, ChIPseqR, ClassifyR, CODEX, coseq, CSAR, CSSQ, DelayedArray, DelayedDataFrame, DESeq2, DEXSeq, DirichletMultinomial, DMCFB, DMCHMM, DMRcaller, epigenomix, epihet, eQTL, ExperimentHubData, ExpressionAtlas, fCCAC, FlowSorted.Blood.EPIC, GA4GHclient, generegulation, GenoGAM, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicScores, GenomicTuples, girafe, groHMM, Gviz, HelloRanges, InPAS, InTAD, IntEREst, IRanges, LoomExperiment, MotifDb, MSnbase, NADfinder, NBAMSeq, OTUbase, padma, 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, plethy, Rcwl, RegEnrich, RepViz, RNAmodR, RnBeads, scDataviz, segmentSeq, SeqGate, SNPlocs.Hsapiens.dbSNP141.GRCh38, Spectra, SQLDataFrame, Structstrings, SummarizedBenchmark, TimeSeriesExperiment, topdownr, TreeSummarizedExperiment, triplex, VariantExperiment, VariantTools, vulcan, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XVector
Imports Me adaptest, ADImpute, affycoretools, aggregateBioVar, ALDEx2, AllelicImbalance, alpine, AlpsNMR, amplican, AneuFinder, animalcules, AnnotationDbi, AnnotationForge, AnnotationHub, annotatr, appreci8R, ArrayTV, ASpediaFI, ASpli, AUCell, BadRegionFinder, ballgown, BASiCS, BasicSTARRseq, batchelor, BayesSpace, BiocIO, BiocNeighbors, BiocOncoTK, BiocSet, BiocSingular, biotmle, biovizBase, biscuiteer, BiSeq, BitSeq, bluster, bnbc, BPRMeth, BrainSABER, branchpointer, breakpointR, BSgenome, bsseq, BUSpaRse, CAGEfightR, CAGEr, casper, CATALYST, cBioPortalData, ccfindR, celaref, celda, CellaRepertorium, celldex, CeTF, cgdv17, CHETAH, ChIC, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPQC, ChIPseeker, chipseqDBData, ChIPSeqSpike, ChromSCape, chromstaR, chromswitch, chromVAR, cicero, CINdex, circRNAprofiler, CiteFuse, cleaver, CluMSID, clusterExperiment, clustifyr, cn.mops, CNEr, CNVPanelizer, CNVRanger, COCOA, CoGAPS, coMET, compEpiTools, ComplexHeatmap, consensusDE, consensusSeekeR, contiBAIT, copynumber, CopywriteR, CoreGx, CoverageView, CRISPRseek, CrispRVariants, csaw, cummeRbund, curatedMetagenomicData, curatedTCGAData, customProDB, cydar, cytomapper, DAMEfinder, dasper, debrowser, DECIPHER, decompTumor2Sig, DEFormats, DegNorm, DEGreport, DelayedMatrixStats, derfinder, derfinderHelper, derfinderPlot, DEScan2, DEWSeq, DiffBind, diffcyt, diffHic, diffloop, DiscoRhythm, dittoSeq, DMRcate, dmrseq, doseR, DRIMSeq, DropletTestFiles, DropletUtils, easyRNASeq, eegc, eisaR, ELMER, ENCODExplorer, ENmix, EnrichmentBrowser, enrichTF, ensembldb, ensemblVEP, EpiTxDb, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomePeak2, ExperimentHub, ExploreModelMatrix, FastqCleaner, fastseg, FilterFFPE, FindMyFriends, fishpond, fitCons.UCSC.hg19, flowCore, FRASER, FunciSNP, GA4GHshiny, gcapc, GDSArray, genbankr, GeneRegionScan, GENESIS, GeneStructureTools, GeneTonic, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicFiles, GenomicInteractions, GenomicOZone, genoset, GGBase, ggbio, GGtools, Glimma, gmapR, gmoviz, GOpro, GOTHiC, gQTLBase, gQTLstats, GRmetrics, GSEABenchmarkeR, GSVA, GUIDEseq, gwascat, h5vc, HCAExplorer, HDF5Array, HiCBricks, HiCcompare, HighlyReplicatedRNASeq, HiLDA, hipathia, hmdbQuery, HMP16SData, HMP2Data, HTSeqGenie, HumanTranscriptomeCompendium, icetea, ideal, ILoReg, IMAS, ImpulseDE2, INSPEcT, InteractionSet, InterMineR, iSEE, iSEEu, isomiRs, IVAS, ivygapSE, IWTomics, JunctionSeq, karyoploteR, kebabs, leeBamViews, lionessR, lipidr, loci2path, LOLA, MACPET, MADSEQ, 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.gnomAD.r3.0.GRCh38, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.r3.0.GRCh38, marr, martini, MAST, mbkmeans, mCSEA, MEAL, meshr, MesKit, metabCombiner, metagenomeFeatures, MetaGxPancreas, metaseqR2, MetCirc, MethCP, methInheritSim, MethReg, methylCC, methylInheritance, methylKit, methylPipe, MethylSeqData, methylSig, methylumi, methyvim, mimager, minfi, MinimumDistance, MIRA, MiRaGE, missMethyl, missRows, MMAPPR2, MMDiff2, Modstrings, mosaics, MOSim, motifbreakR, motifmatchr, MotIV, MouseGastrulationData, mpra, msa, MsCoreUtils, msgbsR, MSPrep, MultiAssayExperiment, MultiDataSet, muscat, musicatk, MutationalPatterns, mygene, myvariant, NanoMethViz, NarrowPeaks, ncRNAtools, nearBynding, netDx, NoRCE, nucleoSim, nucleR, oligoClasses, ontoProc, openPrimeR, ORFik, Organism.dplyr, OrganismDbi, OUTRIDER, packFinder, PAIRADISE, panelcn.mops, PAST, PathwaySplice, pcaExplorer, pd.atdschip.tiling, pdInfoBuilder, periodicDNA, PGA, PharmacoGx, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, phemd, PING, pipeComp, plyranges, pmp, pogos, polyester, pqsfinder, pram, prebs, preciseTAD, PrecisionTrialDrawer, primirTSS, proActiv, procoil, proDA, profileplyr, pulsedSilac, PureCN, PWMEnrich, qcmetrics, QFeatures, qpgraph, QuasR, R3CPET, R453Plus1Toolbox, RadioGx, RaggedExperiment, RareVariantVis, Rariant, Rcade, RCAS, recount, recount3, recountmethylation, recoup, regioneR, regionReport, regsplice, regutools, REMP, Repitools, ResidualMatrix, restfulSE, rexposome, rfaRm, RGMQL, rhdf5client, RiboProfiling, ribor, ribosomeProfilingQC, RJMCMCNucleosomes, RMassBank, Rmmquant, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAprobR, roar, Rqc, Rsamtools, rScudo, RTCGAToolbox, RTN, rtracklayer, SC3, scater, scClassify, scDblFinder, scDD, scds, scHOT, scmap, scMerge, SCnorm, SCOPE, scp, scPipe, scran, scRNAseq, scruff, scTensor, scTGIF, scuttle, SeqArray, seqCAT, seqplots, seqsetvis, SeqSQC, SeqVarTools, sesame, SEtools, sevenbridges, sevenC, SGSeq, ShortRead, SingleCellExperiment, SingleCellMultiModal, singleCellTK, SingleR, singscore, skewr, SMITE, SNPhood, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.GRCh38, soGGi, SomaticCancerAlterations, SomaticSignatures, Spaniel, SpatialExperiment, spatialLIBD, spicyR, splatter, SplicingGraphs, SPLINTER, sRACIPE, srnadiff, STAN, strandCheckR, struct, SummarizedExperiment, SynExtend, TAPseq, TarSeqQC, TBSignatureProfiler, TCGAbiolinks, TCGAutils, TFBSTools, TFHAZ, tidySingleCellExperiment, tidySummarizedExperiment, TileDBArray, TnT, ToxicoGx, trackViewer, tradeSeq, transcriptR, TransView, Trendy, tRNA, tRNAdbImport, tRNAscanImport, TSCAN, tscR, TSRchitect, TVTB, twoddpcr, tximeta, TxRegInfra, Ularcirc, UMI4Cats, universalmotif, VanillaICE, VariantAnnotation, VariantFiltering, vasp, VaSP, VCFArray, velociraptor, VplotR, wavClusteR, weitrix, wiggleplotr, XCIR, xcms, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector, yamss, zellkonverter
Suggests Me alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, BiocGenerics, curatedAdipoChIP, curatedAdipoRNA, dearseq, epivizrChart, globalSeq, GWASTools, GWENA, RTCGA, StructuralVariantAnnotation, TFEA.ChIP, TFutils, tidybulk
Links To Me Biostrings, CNEr, DECIPHER, DegNorm, DelayedArray, GenomicAlignments, GenomicRanges, HDF5Array, IRanges, kebabs, MatrixRider, Rsamtools, rtracklayer, ShortRead, Structstrings, triplex, VariantAnnotation, VariantFiltering, XVector
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Follow Installation instructions to use this package in your R session.

Source Package S4Vectors_0.28.1.tar.gz
Windows Binary S4Vectors_0.28.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) S4Vectors_0.28.1.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/
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Old Source Packages for BioC 3.12 Source Archive