GenomicRanges

DOI:10.18129 / b9.bioc.genomicranges.

基因组间隔的表示和操纵

生物导体版本:发布(3.12)

在分析高通量测序数据(又称NGS数据)时，高效表达和操纵基因组注释和比对的能力发挥着核心作用。基因组范围包定义了用于存储和操作基因组间隔和基因组中定义的变量的通用容器。在genomic alignations和summarizeexperiment包中分别定义了更专门的容器，用于表示和操作参照基因组的短对齐，或者一个类似于矩阵的实验总结。这两个包都构建在GenomicRanges基础架构之上。

作者：P.Aboyoun，H.Pagès和M. Lawrence

维护者：Bioconductor Package维护者

安装

要安装此软件包，请启动R（版本“4.0”）并输入：

如果(!安装BiocManager::install(“基因组范围”)

对于旧版本，请参阅相应的生物导体释放。

文件

要查看系统中安装此包版本的文档，请启动r并输入：

browseVignettes(“GenomicRanges”)

超文本标记语言	R脚本	1.介绍基因组繁文包
PDF.	R脚本	2.GenomicRanges howto
PDF.	R脚本	3.快速介绍GRanges和GRangesList对象(幻灯片)
PDF.	R脚本	4.你不知道的十件事(幻灯片来自BioC 2016)
PDF.	R脚本	5.扩展基因组
PDF.		参考手册
文本		新闻

细节

Biocviews.	2021年欧洲杯 那2021年欧洲杯 那2021年欧洲杯 那2021年欧洲杯 那2021年欧洲杯 那2021年欧洲杯 那2021年欧洲杯 那2021年欧洲杯
版本	1.42.0
在生物导体中以来	BioC 2.6 (R-2.11)(11年)
执照	艺术- 2.0
依靠	R (>= 2.10)， methods, stat4，生物根系（> = 0.25.3），S4Vectors.（> = 0.27.12），IRanges（> = 2.23.9），genomeinfodb.(> = 1.15.2)
进口	utils，stats，xvector.（> = 0.29.2）
链接到	S4Vectors.那IRanges
建议	矩阵那Biobase那annotationdbi.那注释那生物仪器（> = 2.25.3），SummarizedExperiment(> = 0.1.5),RSAMTOOLS.(> = 1.13.53),GenomicAlignments那rtracklayer那bsgenome.那基因组法那Gviz那VariantAnnotation.那annotationhub.那deseq2.那DEXSeq那刨边机那KEGGgraph那rnaseqdata.hnrnpc.bam.chr14.那pasillaBamSubset那KEGG.db那hgu95av2.db那hgu95av2probe.那BSgenome.Scerevisiae.UCSC.sacCer2那BSgenome.Hsapiens.UCSC.hg19那bsgenome.mmusculus.ucsc.mm10那txdb.athalana.biomart.plantsmart22.那TxDb.Dmelanogaster.UCSC.dm3.ensGene那TxDb.Hsapiens.UCSC.hg19.knownGene那TxDb.Mmusculus.UCSC.mm10.knownGene那运行那消化那knitr那BiocStyle
SystemRequirements
加强
URL.	https://biocumon.org/packages/genomicranges.
BugReports	https://github.com/Bioconductor/GenomicRanges/issues
取决于我	AllelicImbalance那AneuFinder那annmap.那AnnotationHubData那BaalChIP那Basic4cseq.那BasicSTARRseq那贝凯那Biomvrcns.那Biseq.那BNBC.那BPRMeth.那断点那bsgenome.那BSSeq.那BubbleTree那bumphunter那咖啡店那CageFightr.那卡斯珀那Champdata.那收费那嵌合体那Chimeraviz那ChIPanalyser那ChIPComp那ChIPpeakAnno那ChIPQC那chipseq.那chromPlot那铬星座那chromswitch那Cindex.那cn.mops.那CNVGSA.那CNVPanelizer.那CNVRanger那可可那COMPETOOLS.那共识那CSAR.那CSAW.那CSSQ那Deepsnv.那DEScan2那deseq2.那DEXSeq那困惑那Diffhic.那DMCFB.那DMCHMM那dmrcaller.那DMRforPairs那dnashaper.那eatonetalchipseq.那enroichedheatmap.那Ensembldb.那Ensemblvep.那epigenomix那epihet那esATAC那EuPathDB那ExCluster那exomeCopy那快速那FCCAC.那FunChIP那GeneBreak那generxcluster.那GenomicAlignments那基因组法那基因组夫妇那GenomicOZone那GenomicScores那GenomicTuples那Genoset.那Geuvstore2.那gmapR那gmoviz那GMRP.那哥特那GreyListChIP那groHMM那gtrellis那GUIDESEQ.那吉他那Gviz那Helloranges.那Hiannotator.那HiTC那德国兹那IGVR.那inpas.那划那intansv那InteractionSet那感兴趣那iwtomics.那Karyploter.那升降机那蒙越者那Mbased.那梅丽莎那metagene那Metagene2.那meth那methyAnalysis那Methylkit.那methylPipe那Minfi.那motifdb.那图案那msgbsR那mutationalpatterns.那NADfinder那OmicCircos那ORFik那periodicDNA那PGA.那plyranges那Podkat.那Quasr.那r3cseq.那raggedexperiment.那Rariant那rcade.那补偿那林那repviz.那rfPred那rGREAT那Riboseqr.那ribosomeProfilingQC那rjmcmcncnucosomes.那RNAmodR那rnbeads.那RnBeads.hg19那RnBeads.hg38那RnBeads.mm10那rnbeads.mm9.那rnbeads.rn5.那RSAMTOOLS.那RSVSim那rtracklayer那scale4c.那SCATEData那范围那Semmentseq.那SEQBIAS.那SEQCAT.那SEQGATE.那测序那SGSEQ.那Sictools.那sigfuge.那击杀那SNPhood那SNPlocs.Hsapiens.dbSNP.20101109那snplocs.hsapiens.dbsnp.20120608.那SNPlocs.Hsapiens.dbSNP141.GRCh38那SNPlocs.Hsapiens.dbSNP142.GRCh37那Somaticsignatures.那StrafturalVariantAnnotation.那SummarizedExperiment那TarSeqQC那TNT.那TrackViewer.那TransView那拖拉器那TRNA.那trnadbimport.那Trnascanimport.那VanillaICE那VariantAnnotation.那VariantExperiment那VariantTools那vplotr.那vtpnet.那vulcan.那波兰人那WGSMAPP.那xtrasnplocs.hsapiens.dbsnp141.grch38.那YAPSA
进口我	高手那ALDEx2那高寒那阿尔卑斯山脉那amplican那AnnotationFilter那annotatr.那APAlyzer那apeglm.那嗯那ArrayExpresshts.那ASpediaFI那Aspli.那评估员那ATACseqQC那BadregionFinder.那舞会礼服那Bambu.那bamsignals那BBCAnalyzer那beadarray那击败那BiFET那Biocio.那Bioconcotk.那Biotip.那biovizBase那biscuiteer那Biseq.那脑流量体面那Branchpointer.那BRGenomics那bsgenome.那海滩那蛋糕那cbioportaldata.那CexoR那cgdv17那冠军那别致那chipenrich那chipenrich.data那ChIPexoQual那Chipseeker.那chipseq.那chipseqr.那ChIPSeqSpike那chromDraw那ChromheatMap.那ChromSCape那Chromvar.那西塞罗那Circrnaprofiler.那Cleanupdtseq.那cn那cnvfilter.那彗星那compartmap那contiBAIT那骗子那CopyNumber.那CopyNumberplots.那撰稿人那COSMIC.67那CoverageView那Crisprseekplus.那CrispRVariants那Customprodb.那DAMEfinder那司布那德布雷斯勒那decomptumor2sig那位深蓝那反编排那DegNorm那deltacapturec那derfinder那derfinderPlot那DEWSeq那diffloop那DMRcate那DMRScan那dmrseq那多米诺骨牌效应那德里姆瑟克那easyrnaseq.那edaseq.那Eisar.那埃尔默那ELMER.data那ENCODExplorer那enrichtf.那EpiTxDb那Epivizr.那epivizrData那erma那EventPointer那exoMepeak2.那fcScan那Filterffpe.那fitcons.ucsc.hg19.那FourCSeq那弗雷泽那FunciSNP那Ga4ghclient.那gcapc那GenBankr.那基因测定那GeneGeneInteR那《创世纪》那GeneStructureTools那genogam.那基因组那GenomeIntervals.那GenomicAlignments那GenomicDataComons.那基因组互动那GenotyPeeval.那Genvisr.那GGBase那GGBIO.那GGtools那GOfuncR那GPART.那gQTLBase那gqtlstats.那gwascat那H5VC那的热图那Hicbricks.那HiCcompare那HilbertCurve那希尔达那HireadsProcessor.那htseqgenie.那蜂鸟那冰茶那理想的那idr2d那IMAS.那检查那潮流器那IPDDB.那IsoformSwitchAnalyzer.那Isomirs.那迭代那iva那JunctionSeq那Karyploter.那leeBamViews那loci2path.那萝拉那索细那lumi.那MACPET那MADSEQ那mafdb.1kgenomes.phase1.grch38.那MafDb.1Kgenomes.phase1.hs37d5那MafDb.1Kgenomes.phase3.GRCh38那mafdb.1kgenomes.phase3.hs37d5.那MafDb.ExAC.r1.0.GRCh38那mafdb.exac.r1.0.hs37d5.那MafDb.ExAC.r1.0.nonTCGA.GRCh38那mafdb.exac.r1.0.nontcga.hs37d5.那MafDb.gnomAD.r2.1.GRCh38那mafdb.gnomad.r2.1.hs37d5.那MafDb.gnomAD.r3.0.GRCh38那MafDb.gnomADex.r2.1.GRCh38那MafDb.gnomADex.r2.1.hs37d5那mafdb.topmed.freeze5.hg19.那mafdb.topmed.freeze5.hg38.那MafH5.gnomAD.r3.0.GRCh38那McSea.那联合化疗那一顿饭那冰雹那Megadepth.那metaseqR2那MethCP那methInheritSim那MethReg那methrix那methyAnalysis那methylCC那methylInheritance那Methylseekr.那methylseqdata.那methylSig那弥撒那MinimumDistance那米拉那MissMethyl.那MMAPPR2那MMDiff2那Modstrings那马赛克那motifbreakR那motifmatchr.那Mousefm.那MultiAssayExperiment那多射线那MultiDataSet那multiHiCcompare那Musicatk.那nanomethviz那ringerpeaks.那ncrnatools.那邻近那netdx.那NoRCE那normr那诊断那oligoclasses.那omadb.那openPrimeR那有机族那OrganismDbi那探险者那Packfinder.那网页排名那Panelcn.mops.那过去的那pcaexplorer.那佩珀纳特那百事可乐那Phastcons100way.ucsc.hg19.那phastcons100way.ucsc.hg38那Phastcons7way.ucsc.hg38那π那图片那p那pqsfinder那摇篮那预先那preciseTAD那PrecisionTrialDrawer那primirTSS那Proactiv.那proBAMr那profflewlactiple.那PureCN那PVIZ.那pwOmics那QDNAseq那QPGraph..那qsea那Qtlizer那R3CPET.那R453Plus1Toolbox那Rarevariantvis.那RCA.那rCGH那重新计票那追叙3.那revountworkflow.那林那RegionReport.那Regutools.那REMP那repitools.那RGADEM.那RGMQL.那Rhisat2.那RiboProfiling那RIPAT那Rmmquant那rnaeditr.那rnamodr.allanilineseq.那rnamodr.ml.那rnamodr.Ribomethseq.那rnaprobr.那rnaseqmap.那咆哮那RTCGAToolbox那SCATE那抚慰那scoreInvHap那SCPIPE.那scrnapeq.那颈背那天窗那seq2pathway.那SEQARRAY.那seqpattern.那seqplots那seqsetvis那SeqSQC那SEQVARTOOLS.那芝麻那塞塞伦那ShortRead那签收那Sigspack.那辛染那Simulatorz.那snapcount.那SNPlocs.Hsapiens.dbSNP.20101109那snplocs.hsapiens.dbsnp.20120608.那SNPlocs.Hsapiens.dbSNP141.GRCh38那SNPlocs.Hsapiens.dbSNP142.GRCh37那snplocs.hsapiens.dbsnp144.grch37.那snplocs.hsapiens.dbsnp144.grch38.那snplocs.hsapiens.dbsnp149.grch38.那snplocs.hsapiens.dbsnp150.grch38.那snplocs.hsapiens.dbsnp151.grch38.那Soggi.那SomaticCancerAlterations那SparseSignatures那SpectralTAD那SplicingGraphs那分裂那srnadiff那斯坦那strandCheckR那Systempiper.那TAPseq那目标那tcgabiolinks.那tcgautils.那TCGAWorkflow那TCseq那TFARM那TFBSTools那TFEA。芯片那TFHAZ那TitanCNA那Tracktables.那经纪人那横向那trena那三层那tscR那Tsrchitect那TVTB.那tximeta那txreginfra.那ularcirc.那umi4cats.那undodapplib.那奥尼润那VariantFiltering那Varianttoolsdata.那vasp那VCFArray那Wiggleplotr.那xtrasnplocs.hsapiens.dbsnp141.grch38.那XtraSNPlocs.Hsapiens.dbSNP144.GRCh37那XtraSNPlocs.Hsapiens.dbSNP144.GRCh38那yrimulti
建议我	alternativeSplicingEvents.hg19那alternativeSplicingEvents.hg38那annotationhub.那beadarrayusecases.那生物室那生物根系那BiocParallel那CageWorkflow.那芝加哥那ComplexHeatMap.那腰带那Epivizrchart.那genomeinfodb.那GenomicState那geuvadistranscriptexpr.那Glimma那Gsreg.那Gwastools.那HDF5Array那interactiveDisplay那IRanges那metaseqR那海市蜃楼那纳米管子那ringerpeaks.那omicsprint.那onassis.那帕尔布斯那彻底甲基化那RNAmodR。数据那RTCGA那S4Vectors.那SeqGSEA那Sesamedata.那single.mtec.transcriptomes.那飞溅那tfutils.
我的链接
构建报告

包档案

遵循2021年欧洲杯比分预测 在r会话中使用此包的说明。

源包	GenomicRanges_1.42.0.tar.gz
Windows二进制	genomicranges_1.42.0.zip.
macOS 10.13 (High Sierra)	GenomicRanges_1.42.0.tgz
源存储库	git克隆https://git.bioconductor.org/packages/GenomicRanges
源存储库(开发人员访问)	git clone git@git.biocondion.org：包/基因组ranges
包短Url	https://biocumon.org/packages/genomicranges/
包裹下载报告	下载数据