GenomicRanges

DOI:10.18129 / B9.bioc.GenomicRanges

这个包是3.13版本Bioconductor;的稳定,最新的发布版本,请参阅GenomicRanges

表示和操纵基因间隔

Bioconductor版本:3.13

能够有效地表示和操纵基因注释和校准时发挥着核心作用分析高通量测序数据(或称门店数据)。GenomicRanges包定义了通用的容器存储和操纵基因间隔和变量定义在一个基因组。更专业的容器代表和操纵短对参考基因组比对,或表来总结一个实验,分别GenomicAlignments和SummarizedExperiment包中定义的。两个包之上构建GenomicRanges基础设施。

作者:p . Aboyoun h .页,和m .劳伦斯

维修工:Bioconductor包维护者<维护者bioconductor.org >

从内部引用(R,回车引用(“GenomicRanges”)):

安装

安装这个包,开始R(版本“4.1”)并输入:

如果(!requireNamespace (“BiocManager”,悄悄地= TRUE)) install.packages (“BiocManager”) BiocManager::安装(“GenomicRanges”)

R的旧版本,请参考适当的Bioconductor释放

文档

查看文档的版本这个包安装在您的系统,开始R和输入:

browseVignettes (“GenomicRanges”)

HTML R脚本 1。介绍GenomicRanges包
PDF R脚本 2。GenomicRanges howto
PDF R脚本 3所示。简单介绍农庄和GRangesList对象(幻灯片)
PDF R脚本 4所示。十件你不知道(从2016年BioC幻灯片)
PDF R脚本 5。延长GenomicRanges
PDF 参考手册
文本 新闻

细节

biocViews 注释,报道,DataRepresentation,遗传学,GenomeAnnotation,基础设施,测序,软件
版本 1.44.0
Bioconductor自 BioC 2.6 (r - 2.11)(11.5年)
许可证 艺术- 2.0
取决于 R(> = 4.0.0)、方法stats4,BiocGenerics(> = 0.37.0),S4Vectors(> = 0.27.12),IRanges(> = 2.23.9),GenomeInfoDb(> = 1.15.2)
进口 跑龙套,统计数据,XVector(> = 0.29.2)
链接 S4Vectors,IRanges
建议 矩阵,Biobase,AnnotationDbi,注释,Biostrings(> = 2.25.3),SummarizedExperiment(> = 0.1.5),Rsamtools(> = 1.13.53),GenomicAlignments,rtracklayer,BSgenome,GenomicFeatures,Gviz,VariantAnnotation,AnnotationHub,DESeq2,DEXSeq,刨边机,KEGGgraph,RNAseqData.HNRNPC.bam.chr14,pasillaBamSubset,KEGGREST,hgu95av2.db,hgu95av2probe,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Hsapiens.UCSC.hg19,BSgenome.Mmusculus.UCSC.mm10,TxDb.Athaliana.BioMart.plantsmart22,TxDb.Dmelanogaster.UCSC.dm3.ensGene,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene,RUnit,消化,knitr,rmarkdown,BiocStyle
SystemRequirements
增强了
URL //www.anjoumacpherson.com/packages/GenomicRanges
BugReports https://github.com/Bioconductor/GenomicRanges/issues
取决于我 AllelicImbalance,AneuFinder,annmap,AnnotationHubData,BaalChIP,Basic4Cseq,BasicSTARRseq,baySeq,biomvRCNS,BiSeq,bnbc,BPRMeth,breakpointR,BSgenome,bsseq,BubbleTree,bumphunter,咖啡馆,CAGEfightR,卡斯珀,ChAMPdata,chimeraviz,ChIPanalyser,ChIPComp,ChIPpeakAnno,ChIPQC,chipseq,chromPlot,chromstaR,chromswitch,CINdex,cn.mops,cnvGSA,CNVPanelizer,CNVRanger,可可,compEpiTools,consensusSeekeR,CSAR,csaw,CSSQ,deepSNV,DEScan2,DESeq2,DEXSeq,DiffBind,diffHic,DMCFB,DMCHMM,DMRcaller,DMRforPairs,DNAshapeR,EatonEtAlChIPseq,EnrichedHeatmap,ensembldb,ensemblVEP,epigenomix,epihet,esATAC,EuPathDB,ExCluster,exomeCopy,fastseg,fCCAC,FunChIP,GeneBreak,geneRxCluster,GenomicAlignments,GenomicDistributions,GenomicFeatures,GenomicFiles,GenomicOZone,GenomicScores,GenomicTuples,genoset,gmapR,gmoviz,GMRP,哥特,GreyListChIP,groHMM,gtrellis,GUIDEseq,吉他,Gviz,HelloRanges,hiAnnotator,HiTC,IdeoViz,igvR,InPAS,InTAD,intansv,InteractionSet,感兴趣,IWTomics,karyoploteR,liftOver,微波激射器,工商管理硕士,梅丽莎,metagene,metagene2,methimpute,methyAnalysis,methylKit,methylPipe,minfi,MotifDb,msgbsR,MutationalPatterns,NADfinder,OmicCircos,ORFik,periodicDNA,plyranges,podkat,QuasR,r3Cseq,RaggedExperiment,ramr,Rcade,收回,地区,RepViz,rfPred,rGREAT,riboSeqR,ribosomeProfilingQC,RJMCMCNucleosomes,RNAmodR,RnBeads,RnBeads.hg19,RnBeads.hg38,RnBeads.mm10,RnBeads.mm9,RnBeads.rn5,Rsamtools,RSVSim,rtracklayer,Scale4C,SCATEData,范围,segmentSeq,seqbias,seqCAT,SeqGate,测序,SGSeq,SICtools,SigFuge,击杀,SNPhood,SNPlocs.Hsapiens.dbSNP.20101109,SNPlocs.Hsapiens.dbSNP.20120608,SNPlocs.Hsapiens.dbSNP141.GRCh38,SNPlocs.Hsapiens.dbSNP142.GRCh37,SomaticSignatures,StructuralVariantAnnotation,SummarizedExperiment,TarSeqQC,三硝基甲苯,trackViewer,TransView,tra利用,tRNA,tRNAdbImport,tRNAscanImport,VanillaICE,VarCon,VariantAnnotation,VariantExperiment,VariantTools,VplotR,vtpnet,火神,wavClusteR,WGSmapp,XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,YAPSA
进口我 王牌,ALDEx2,高山,阿尔卑斯山脉,amplican,AnnotationFilter,annotatr,APAlyzer,apeglm,appreci8R,ArrayExpressHTS,ASpediaFI,ASpli,AssessORF,ATACseqQC,BadRegionFinder,舞会礼服,bambu,bamsignals,BBCAnalyzer,beadarray,击败,BiFET,BiocOncoTK,BioTIP,biovizBase,biscuiteer,BiSeq,brainflowprobes,分歧点,BRGenomics,BSgenome,BUSpaRse,篮球选手,cBioPortalData,CexoR,cgdv17,冠军,别致的,chipenrich,chipenrich.data,ChIPexoQual,ChIPseeker,chipseq,ChIPseqR,ChIPSeqSpike,chromDraw,ChromHeatMap,ChromSCape,chromVAR,西塞罗,circRNAprofiler,cleanUpdTSeq,cn,CNVfilteR,CNViz,彗星,compartmap,contiBAIT,conumee,copynumber,CopyNumberPlots,文案,COSMIC.67,CoverageView,crisprseekplus,CrispRVariants,customProDB,DAMEfinder,dasper,debrowser,decompTumor2Sig,位深蓝,反编排,DegNorm,deltaCaptureC,derfinder,derfinderPlot,DEWSeq,diffloop,diffUTR,DMRcate,DMRScan,dmrseq,DominoEffect,DRIMSeq,easyRNASeq,EDASeq,eisaR,埃尔默,ELMER.data,ENCODExplorer,enrichTF,epialleleR,epidecodeR,epigraHMM,EpiTxDb,epivizr,epivizrData,erma,EventPointer,exomePeak2,fcScan,FilterFFPE,fitCons.UCSC.hg19,弗雷泽,GA4GHclient,gcapc,genbankr,geneAttribution,GeneGeneInteR,《创世纪》,GeneStructureTools,GenoGAM,genomation,genomeIntervals,GenomicAlignments,GenomicDataCommons,GenomicDistributionsData,GenomicInteractions,genotypeeval,GenVisR,ggbio,GOfuncR,gpart软件,gwascat,h5vc,的热图,HiCBricks,HiCcompare,HiCDCPlus,HilbertCurve,希尔达,hiReadsProcessor,HTSeqGenie,蜂鸟,icetea,理想的,idr2d,ima,检查,InterMineR,ipdDb,IsoformSwitchAnalyzeR,isomiRs,iteremoval,iva,karyoploteR,leeBamViews,loci2path,萝拉,LoomExperiment,光民,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,MafH5.gnomAD.v3.1.1.GRCh38,mCSEA,联合化疗,,MEDIPS,megadepth,模因,metaseqR2,MethCP,methInheritSim,MethReg,methrix,methyAnalysis,methylCC,methylInheritance,MethylSeekR,MethylSeqData,methylSig,methylumi,MinimumDistance,米拉,missMethyl,MMAPPR2,MMDiff2,Modstrings,马赛克,motifbreakR,motifmatchr,MouseFM,MultiAssayExperiment,multicrispr,MultiDataSet,multiHiCcompare,MungeSumstats,musicatk,NanoMethViz,ncRNAtools,nearBynding,netDx,NoRCE,normr,诊断,oligoClasses,OmaDB,openPrimeR,Organism.dplyr,OrganismDbi,先驱者,packFinder,网页排名,panelcn.mops,过去的,pcaExplorer,pepDat,pepStat,phastCons100way.UCSC.hg19,phastCons100way.UCSC.hg38,phastCons7way.UCSC.hg38,PhIPData,π,图片,,pqsfinder,婴儿车,prebs,preciseTAD,PrecisionTrialDrawer,primirTSS,高伦雅芙,proBAMr,profileplyr,PureCN,Pviz,pwOmics,QDNAseq,qpgraph,qsea,Qtlizer,R3CPET,R453Plus1Toolbox,RareVariantVis,美国广播公司,