Movatterモバイル変換

[0]ホーム
URL:

Bioconductor 3.22 Released

Bioconductor home
Menu

S4Vectors

This is thereleased version of S4Vectors; for the devel version, seeS4Vectors.

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

Platform availability badgeRanking badgeSupport activity badgeYears in BioConductor badgeBuild results badgeLast commit badgeDependency count badge

DOI: 10.18129/B9.bioc.S4Vectors


Bioconductor version: Release (3.22)

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, entercitation("S4Vectors")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")BiocManager::install("S4Vectors")

For older versions of R, please refer to the appropriateBioconductor 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 systemHTMLR Script
An Overview of the S4Vectors packageHTMLR Script
Rle Tips and TricksHTMLR Script
Reference ManualPDF
NEWSText

Need some help? Ask on the Bioconductor Support site!

Details

biocViewsDataRepresentation,Infrastructure,Software
Version0.48.0
In Bioconductor sinceBioC 3.0 (R-3.1) (11 years)
LicenseArtistic-2.0
DependsR (>= 4.0.0), methods, utils, stats, stats4,BiocGenerics(>= 0.53.2)
Imports
System Requirements
URLhttps://bioconductor.org/packages/S4Vectors
Bug Reportshttps://github.com/Bioconductor/S4Vectors/issues
See More
SuggestsIRanges,GenomicRanges,SummarizedExperiment,Matrix,DelayedArray,ShortRead,graph,data.table,RUnit,BiocStyle,knitr
Linking To
Enhances
Depends On Mealtcdfenvs,AnnotationHubData,ATACseqQC,bambu,bandle,betaHMM,Biostrings,BiSeq,BSgenome,bumphunter,Cardinal,CellMapper,CexoR,chimeraviz,ChIPpeakAnno,chipseq,ChIPseqR,cigarillo,ClassifyR,cliProfiler,CODEX,CompoundDb,coseq,CSAR,CSSQ,DelayedArray,DelayedDataFrame,DESeq2,DEXSeq,DirichletMultinomial,DMCFB,DMCHMM,DMRcaller,ExperimentHubData,ExpressionAtlas,fCCAC,GA4GHclient,GenomeInfoDb,GenomicAlignments,GenomicFeatures,GenomicRanges,GenomicScores,GenomicTuples,GeomxTools,groHMM,Gviz,hdxmsqc,HelloRanges,HERON,InTAD,IntEREst,IRanges,linkSet,LoomExperiment,m6Aboost,MetNet,MotifDb,MSnbase,MuData,MultimodalExperiment,NADfinder,NanoStringNCTools,NBAMSeq,octad,OGRE,OTUbase,padma,PSMatch,pwalign,Rcwl,RegEnrich,RNAmodR,RnBeads,S4Arrays,scDataviz,screenCounter,segmentSeq,SeqGate,SparseArray,Spectra,strandCheckR,Structstrings,topdownr,TreeSummarizedExperiment,TRESS,triplex,txdbmaker,updateObject,VariantExperiment,VariantTools,vulcan,XVector,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 MeADImpute,adverSCarial,affycoretools,aggregateBioVar,airpart,alabaster.base,alabaster.bumpy,alabaster.files,alabaster.mae,alabaster.matrix,alabaster.ranges,alabaster.se,alabaster.sfe,alabaster.spatial,alabaster.string,alabaster.vcf,ALDEx2,AllelicImbalance,amplican,anansi,anglemania,animalcules,AnnotationDbi,AnnotationForge,AnnotationHub,annotatr,appreci8R,ASpli,ASURAT,ATACseqTFEA,atena,autonomics,BadRegionFinder,ballgown,Banksy,barbieQ,BASiCS,batchelor,BatchQC,BayesSpace,bettr,BindingSiteFinder,Bioc.gff,BiocHubsShiny,BiocIO,BiocSet,BiocSingular,biotmle,biovizBase,biscuiteer,BiSeq,bluster,bnbc,breakpointR,BREW3R.r,BSgenomeForge,bsseq,BumpyMatrix,BUSpaRse,BUSseq,CAGEfightR,CAGEr,cardelino,CardinalIO,CARDspa,casper,CATALYST,CatsCradle,cBioPortalData,ccfindR,celaref,celda,CellBarcode,censcyt,Cepo,CeTF,cfdnakit,CHETAH,chevreulPlot,chevreulProcess,chevreulShiny,chipenrich,ChIPexoQual,ChIPseeker,Chromatograms,ChromSCape,chromVAR,cicero,circRNAprofiler,CircSeqAlignTk,CiteFuse,cleanUpdTSeq,cleaver,CluMSID,clusterExperiment,clustifyr,cn.mops,CNEr,CNVMetrics,CNVPanelizer,CNVRanger,COCOA,CoGAPS,Cogito,compEpiTools,consensusDE,consensusSeekeR,Coralysis,CoreGx,CoverageView,crisprBase,crisprDesign,CRISPRseek,crisprShiny,CrispRVariants,crisprViz,crupR,csaw,CTDquerier,CuratedAtlasQueryR,cydar,cytoKernel,cytomapper,cytoviewer,DAMEfinder,dandelionR,debrowser,DECIPHER,decompTumor2Sig,decontX,DeconvoBuddies,deconvR,DeeDeeExperiment,DEFormats,DegCre,DegNorm,DEGreport,DelayedMatrixStats,derfinder,derfinderHelper,derfinderPlot,DEScan2,DESpace,DEWSeq,DFplyr,DiffBind,diffcyt,diffHic,diffUTR,Dino,DiscoRhythm,dittoSeq,DMRcaller,DMRcate,dmrseq,DNAfusion,doseR,DOtools,dreamlet,DRIMSeq,DropletUtils,drugTargetInteractions,DspikeIn,dStruct,easyRNASeq,eisaR,ELMER,enhancerHomologSearch,EnrichDO,EnrichmentBrowser,ensembldb,epigraHMM,EpiMix,epimutacions,epiregulon,epistack,EpiTxDb,epivizr,epivizrData,epivizrStandalone,esATAC,EventPointer,ExperimentHub,ExperimentSubset,ExploreModelMatrix,extraChIPs,FastqCleaner,fastseg,FilterFFPE,FindIT2,fishpond,FLAMES,flowCore,flowWorkspace,FRASER,FuseSOM,G4SNVHunter,GA4GHshiny,gcapc,gDNAx,gDRcore,gDRimport,gDRutils,GDSArray,gemma.R,GeneRegionScan,GENESIS,GeneTonic,genomation,GenomAutomorphism,genomeIntervals,GenomicAlignments,GenomicFiles,GenomicInteractionNodes,GenomicInteractions,GenomicOZone,GenomicSuperSignature,geomeTriD,GEOquery,ggbio,Glimma,glmGamPoi,gmapR,gmoviz,GOpro,GOTHiC,GRaNIE,GRmetrics,GSEABenchmarkeR,GSVA,GUIDEseq,gwascat,h5mread,h5vc,HDF5Array,hermes,HicAggR,HiCaptuRe,HiCBricks,HiCcompare,HiCDOC,HiCExperiment,HiContacts,HiCParser,HiCPotts,hicVennDiagram,HiLDA,hmdbQuery,HoloFoodR,icetea,ideal,IFAA,igblastr,ILoReg,imcRtools,InPAS,INSPEcT,InteractionSet,InteractiveComplexHeatmap,iSEE,iSEEde,iSEEhub,iSEEpathways,iSEEtree,iSEEu,IsoBayes,IsoformSwitchAnalyzeR,IVAS,ivygapSE,karyoploteR,katdetectr,kebabs,kmcut,knowYourCG,lefser,lemur,limpca,LimROTS,lionessR,lipidr,lisaClust,loci2path,LOLA,MACSr,magpie,MAI,mariner,marr,MAST,mbkmeans,mCSEA,MEAL,meshr,MesKit,metabCombiner,MetaboAnnotation,MetaboDynamics,metaseqR2,MetCirc,methInheritSim,methodical,MethReg,methrix,methylCC,methylInheritance,methylKit,methylPipe,methylSig,methylumi,MGnifyR,mia,miaDash,miaSim,miaTime,miaViz,MICSQTL,midasHLA,miloR,mimager,minfi,MinimumDistance,MIRA,MiRaGE,missMethyl,missRows,mist,mitoClone2,MMDiff2,moanin,mobileRNA,Modstrings,MoleculeExperiment,monaLisa,mosaics,MOSClip,mosdef,MOSim,Motif2Site,motifbreakR,motifmatchr,MotifPeeker,motifTestR,MPAC,mpra,msa,MsBackendMassbank,MsBackendMetaboLights,MsBackendMgf,MsBackendMsp,MsBackendRawFileReader,MsBackendSql,MsCoreUtils,MsExperiment,msgbsR,MSPrep,MuData,MultiAssayExperiment,MultiDataSet,MultiRNAflow,multistateQTL,mumosa,muscat,musicatk,MutationalPatterns,mutscan,mygene,myvariant,NanoMethViz,ncRNAtools,nearBynding,notame,nucleoSim,nucleR,nullranges,oligoClasses,omicsGMF,omicsViewer,oncoscanR,ontoProc,openPrimeR,ORFik,Organism.dplyr,OrganismDbi,orthos,OUTRIDER,OutSplice,packFinder,PAIRADISE,pairedGSEA,panelcn.mops,PAST,pcaExplorer,PDATK,pdInfoBuilder,Pedixplorer,periodicDNA,pgxRpi,PharmacoGx,PhIPData,PhosR,PICB,pipeComp,Pirat,plyinteractions,plyranges,plyxp,pmp,pogos,PolySTest,pqsfinder,pram,prebs,preciseTAD,primirTSS,proActiv,procoil,proDA,PRONE,ProteoDisco,PureCN,PWMEnrich,qcmetrics,QFeatures,qpgraph,qsea,QTLExperiment,QuasR,R3CPET,RadioGx,raer,RaggedExperiment,RAIDS,ramr,RareVariantVis,RBioFormats,RCAS,RcisTarget,RcwlPipelines,recount,recount3,recountmethylation,recoup,ReducedExperiment,RegionalST,regioneR,regionReport,regsplice,regutools,REMP,ResidualMatrix,RESOLVE,ReUseData,rexposome,rfaRm,RFLOMICS,RgnTX,rGREAT,RiboDiPA,RiboProfiling,ribor,riboSeqR,ribosomeProfilingQC,rifi,rifiComparative,RJMCMCNucleosomes,RMassBank,Rmmquant,rnaEditr,RNAmodR.AlkAnilineSeq,RNAmodR.ML,RNAmodR.RiboMethSeq,roar,rprimer,Rqc,Rsamtools,rScudo,RTCGAToolbox,RTN,rtracklayer,RUCova,SanityR,saseR,SC3,scafari,ScaledMatrix,scanMiR,scanMiRApp,SCArray,SCArray.sat,scater,scClassify,scDblFinder,scDD,scds,scGraphVerse,scHOT,scider,scmap,scMerge,scMET,SCnorm,SCOPE,scp,scPipe,scran,scRepertoire,scRNAseqApp,scruff,scTensor,scTGIF,scTreeViz,scuttle,scviR,sechm,segmenter,SeqArray,seqCAT,Seqinfo,seqsetvis,SeqSQC,SeqVarTools,sesame,SEtools,sevenbridges,sevenC,SGSeq,shinyDSP,ShortRead,simona,simPIC,simpleSeg,SingleCellAlleleExperiment,SingleCellExperiment,singleCellTK,SingleMoleculeFootprinting,SingleR,singscore,sitadela,Site2Target,skewr,slingshot,SMITE,SNPhood,SomaticSignatures,SOMNiBUS,sosta,SpaceTrooper,Spaniel,SpaNorm,SpatialExperiment,SpatialExperimentIO,spatialFDA,SpatialFeatureExperiment,SpatialOmicsOverlay,SpectriPy,SPICEY,spicyR,spiky,spillR,splatter,SpliceWiz,SplicingGraphs,SplineDV,SPLINTER,SpotClean,sRACIPE,srnadiff,STADyUM,standR,Statial,StructuralVariantAnnotation,SummarizedExperiment,svaNUMT,svaRetro,SVP,SynExtend,systemPipeR,tadar,TAPseq,TBSignatureProfiler,TCGAbiolinks,TCGAutils,TENET,TENxIO,TEQC,terraTCGAdata,TFBSTools,TFHAZ,tidybulk,tidyCoverage,tidySingleCellExperiment,tidySpatialExperiment,tidySummarizedExperiment,TileDBArray,TnT,ToxicoGx,trackViewer,tradeSeq,TrajectoryUtils,transcriptR,transmogR,treeclimbR,Trendy,tricycle,tRNA,tRNAdbImport,tRNAscanImport,TSCAN,TVTB,twoddpcr,txcutr,tximeta,UCSC.utils,Ularcirc,UMI4Cats,universalmotif,UPDhmm,VanillaICE,VariantAnnotation,VariantFiltering,VaSP,VCFArray,VDJdive,velociraptor,VisiumIO,visiumStitched,vmrseq,Voyager,VplotR,wavClusteR,weitrix,wiggleplotr,xcms,xcore,XeniumIO,xenLite,XVector,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.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,bugphyzz,celldex,chipenrich.data,chipseqDBData,curatedMetagenomicData,curatedTCGAData,DNAZooData,DoReMiTra,DropletTestFiles,FlowSorted.Blood.EPIC,fourDNData,HCATonsilData,HighlyReplicatedRNASeq,HMP16SData,HMP2Data,homosapienDEE2CellScore,imcdatasets,leeBamViews,LegATo,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,HiCociety,hicream,hoardeR,imcExperiment,karyotapR,LoopRig,MetAlyzer,microbial,mikropml,multimedia,NIPTeR,PlasmaMutationDetector,restfulr,rliger,rnaCrosslinkOO,rsolr,scROSHI,Signac,TaxaNorm,toxpiR
Suggests MeAlphaMissenseR,AlpsNMR,ANCOMBC,anndataR,BiocGenerics,CCAFE,chihaya,COTAN,dearseq,epiregulon.extra,epivizrChart,GeoTcgaData,globalSeq,GWASTools,GWENA,gypsum,iscream,koinar,maftools,martini,MicrobiotaProcess,MsQuality,MungeSumstats,RTCGA,scrapper,SpectraQL,SPOTlight,TFEA.ChIP,TFutils,XAItest,alternativeSplicingEvents.hg19,alternativeSplicingEvents.hg38,BioPlex,curatedAdipoChIP,curatedAdipoRNA,ObMiTi,xcoredata,dependentsimr,gkmSVM,grandR,inDAGO,LorMe,pmartR,polyRAD,pQTLdata,RCPA,Rgff,Seurat,SNPassoc,updog,valr
Links To MeBioc.gff,Biostrings,cigarillo,CNEr,DECIPHER,DelayedArray,GenomicAlignments,GenomicRanges,h5mread,IRanges,kebabs,MatrixRider,pwalign,Rsamtools,rtracklayer,S4Arrays,ShortRead,SparseArray,Structstrings,triplex,VariantAnnotation,VariantFiltering,XVector
Build ReportBuild Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source PackageS4Vectors_0.48.0.tar.gz
Windows Binary (x86_64) S4Vectors_0.48.0.zip
macOS Binary (x86_64)S4Vectors_0.48.0.tgz
macOS Binary (arm64)S4Vectors_0.48.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/S4Vectors
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/S4Vectors
Bioc Package Browserhttps://code.bioconductor.org/browse/S4Vectors/
Package Short Urlhttps://bioconductor.org/packages/S4Vectors/
Package Downloads ReportDownload Stats
[8]ページ先頭
©2009-2025 Movatter.jp