基因组机

doi:10.18129/b9.bioc.genomicranges

该包适用于生物导体的3.8版;对于稳定的最新版本,请参阅基因组机

沿基因组定义的基因组间隔和变量的表示和操纵

生物导体版本:3.8

在分析高通量测序数据(又称NGS数据)时,有效表示和操纵基因组注释和比对的能力正在发挥核心作用。Genomicranges软件包定义了用于存储和操纵基因组定义的基因组间隔和变量的通用容器。分别在基因组签名和摘要套件中定义了更专业的容器,用于代表和操纵针对参考基因组或实验的基质样摘要的简短对齐。这两个软件包都建立在基因组基础架构之上。

作者:P。Aboyoun,H。Pagès和M. Lawrence

维护者:bioconductor.org>的生物导体套件维护器<维护器>

引用(从r内,输入引用(“基因组”)):

安装

要安装此软件包,请启动R(版本“ 3.5”)并输入:

if(!sireseenamespace(“ biocmanager”,悄悄= true))install.packages(“ biocmanager”)biocmanager :: install(“ genomicranges”)

对于R的较旧版本,请参考适当的生物导体释放

文档

要查看系统中安装此软件包的版本的文档,请启动R并输入:

Browsevignettes(“基因组旋翼”)

html R脚本 1.基因组包装的简介
PDF R脚本 2. Genomicranges Howtos
PDF R脚本 3.快速介绍Granges和GrangeSlist对象(幻灯片)
PDF R脚本 4.您不知道的十件事(Bioc 2016年幻灯片)
PDF R脚本 5.扩展基因组
PDF 参考手册
文本 消息

细节

生物浏览 注解,,,,覆盖范围,,,,遗传学,,,,基因数,,,,基础设施,,,,测序,,,,软件
版本 1.34.0
在生物导体中 Bioc 2.6(R-2.11)(9年)
执照 艺术2.0
要看 r(> = 2.10),方法,stats4,生物基因(> = 0.25.3),S4VECTORS(> = 0.19.11),iranges(> = 2.15.12),GenomeInfodB(> = 1.15.2)
进口 UTIT,统计,xvector(> = 0.19.8)
链接 S4VECTORS,,,,iranges
建议 矩阵,,,,生物酶,,,,AnnotationDbi,,,,注释,,,,生物弦(> = 2.25.3),总结性特征(> = 0.1.5),rsamtools(> = 1.13.53),基因组签名,,,,rtracklayer,,,,BSGENOME,,,,GenomicFeatures,,,,GVIZ,,,,变体,,,,AnnotationHub,,,,deseq2,,,,dexseq,,,,EDGER,,,,kegggraph,,,,rnaseqdata.hnrnpc.bam.chr14,,,,pasillabamsubset,,,,kegg.db,,,,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,,,,txdb.mmusculus.ucsc.mm10.nowngene,,,,运行,,,,消化,,,,尼特,,,,生物使用
系统要求
增强
URL
取决于我 等位基因平衡,,,,Aneufinder,,,,Annmap,,,,AnnotationHubdata,,,,Baalchip,,,,basic4cseq,,,,BasicStarrseq,,,,贝塞克,,,,Biomvrcns,,,,Biseq,,,,BNBC,,,,bprmeth,,,,Breakpointr,,,,BSGENOME,,,,BSSEQ,,,,气泡,,,,Bumphunter,,,,咖啡店,,,,Cagefightr,,,,卡斯珀,,,,Champdata,,,,收费,,,,嵌合体,,,,Chimeraviz,,,,chipanalyser,,,,芯片,,,,Chippeakanno,,,,chipqc,,,,chipseq,,,,chrogps,,,,Chromplot,,,,Chromstar,,,,Chromswitch,,,,Cindex,,,,清理,,,,CN. -ops,,,,cnpbayes,,,,CNVGSA,,,,cnvpanelizer,,,,可可,,,,Compepitools,,,,共识,,,,CSAR,,,,CSAW,,,,Deepsnv,,,,DESCAN2,,,,deseq2,,,,dexseq,,,,差异,,,,Diffhic,,,,dmchmm,,,,DMRCALLER,,,,dmrcatedata,,,,dmrforpairs,,,,dnashaper,,,,doqtl,,,,Eatonetalchipseq,,,,富集图,,,,Ensembldb,,,,ememblvep,,,,Epgenomix,,,,esatac,,,,eupathdb,,,,DEBLUSTER,,,,外观复制,,,,fastseg,,,,FCCAC,,,,Fourcseq,,,,Funchip,,,,吉恩·布雷克(Genebreak),,,,代理商,,,,基因组签名,,,,GenomicFeatures,,,,Genomicfiles,,,,GenomicsCores,,,,基因组菌,,,,Genoset,,,,geuvstore2,,,,GMAPR,,,,GMRP,,,,哥特,,,,Greylistchip,,,,grohmm,,,,Gtrellis,,,,Guideseq,,,,吉他,,,,GVIZ,,,,Helloranges,,,,Hiannotator,,,,HITC,,,,htseqtools,,,,IDEOVIZ,,,,IGVR,,,,inpas,,,,intad,,,,Intansv,,,,互动集,,,,兴趣,,,,iWtomics,,,,核粒子,,,,举起,,,,马瑟,,,,mbased,,,,metagene,,,,甲基,,,,甲基分析,,,,甲基库,,,,甲基管,,,,Minfi,,,,MSGBSR,,,,突变模式,,,,NADFINDER,,,,Omiccircos,,,,ORFIK,,,,PGA,,,,ping,,,,plyranges,,,,podkat,,,,,,,,R3CSEQ,,,,破烂的经历,,,,稀有,,,,rcade,,,,补偿,,,,区域人,,,,rfpred,,,,rgreat,,,,riboseqr,,,,Ripseeker,,,,RJMCMCN核小体,,,,rnbeads,,,,rnbeads.hg19,,,,rnbeads.hg38,,,,rnbeads.mm10,,,,rnbeads.mm9,,,,rnbeads.rn5,,,,rsamtools,,,,RSVSIM,,,,rtracklayer,,,,比例4C,,,,片段,,,,seqbias,,,,seqcat,,,,测序,,,,sgseq,,,,Sictools,,,,sigfuge,,,,Smite,,,,Snphood,,,,snplocs.hsapiens.dbsnp.20101109,,,,snplocs.hsapiens.dbsnp.20120608,,,,snplocs.hsapiens.dbsnp141.grch38,,,,snplocs.hsapiens.dbsnp142.grch37,,,,躯体签名,,,,总结性特征,,,,tarseqqc,,,,TNT,,,,TrackViewer,,,,transview,,,,Traser,,,,tRNA,,,,Trnadbimport,,,,Trnascanimport,,,,香草,,,,变体,,,,变体工具,,,,vtpnet,,,,瓦肯,,,,Wavcluster,,,,xtrasnplocs.hsapiens.dbsnp141.grch38,,,,yapsa
进口我 ALDEX2,,,,高山,,,,扩增器,,,,AnnotationFilter,,,,Annotatr,,,,apeglm,,,,感谢,,,,arrayexpresshts,,,,阿斯普利,,,,评估员,,,,atacseqqc,,,,不良区域,,,,舞会礼服,,,,bamsignals,,,,BBCANALYZER,,,,Beadarray,,,,,,,,比法特,,,,Bioconcotk,,,,Biovizbase,,,,Biseq,,,,分支机构,,,,BSGENOME,,,,卡格,,,,cexor,,,,CGDV17,,,,冠军,,,,时尚,,,,Chipenrich,,,,chipenrich.data,,,,chipexoqual,,,,Chipseeker,,,,chipseq,,,,chipseqr,,,,chipseqspike,,,,ChromDraw,,,,ChromheatMap,,,,Chromvar,,,,西塞罗,,,,CNER,,,,彗星,,,,carpartmap,,,,contibait,,,,Conumee,,,,库务,,,,copywriter,,,,宇宙67,,,,CoverageView,,,,CRISPRSEEKPLUS,,,,crisprvariants,,,,CustomProdb,,,,dchiprep,,,,碎片器,,,,深布鲁尔,,,,变形,,,,德芬德,,,,derfinderplot,,,,diffloop,,,,dmrcate,,,,DMRSCAN,,,,DMRSEQ,,,,多米诺骨牌效应,,,,Drimseq,,,,EasyRnaseq,,,,EDASEQ,,,,埃尔默,,,,Elmer.Data,,,,epivizr,,,,epivizrdata,,,,Erma,,,,EventPointer,,,,FitCons.UCSC.HG19,,,,拖鞋,,,,Fourcseq,,,,funcisnp,,,,ga4ghclient,,,,GCAPC,,,,GenBankr,,,,基因贡献,,,,Genegeneinter,,,,创世纪,,,,GenStructurotootools,,,,Genogam,,,,基因组化,,,,基因组合,,,,基因组签名,,,,GenomicDataCommons,,,,基因组间,,,,Genotypeeval,,,,Genvisr,,,,GGBASE,,,,GGBIO,,,,ggtools,,,,Gofuncr,,,,GoogleGenomics,,,,GPART,,,,GQTLBASE,,,,gqtlstats,,,,Gwascat,,,,H5VC,,,,热图,,,,打ic,,,,Hiccompare,,,,Hilbertcurve,,,,Hireadsprocessor,,,,htseqgenie,,,,冰茶,,,,理想的,,,,IMAS,,,,检查,,,,Interminer,,,,IPDDB,,,,同工型间分析仪,,,,Isomirs,,,,迭代,,,,IVAS,,,,接口,,,,核粒子,,,,Leebamviews,,,,loci2path,,,,萝拉,,,,loomexpermiment,,,,Lumi,,,,M3D,,,,Macpet,,,,Madseq,,,,mafdb.1kgenomes.phase1.grch38,,,,mafdb.1kgenomes.phase1.hs37d5,,,,mafdb.1kgenomes.phase3.grch38,,,,mafdb.1kgenomes.phase3.hs37d5,,,,mafdb.esp6500si.v2.ssa137.grch38,,,,mafdb.esp6500si.v2.ssa137.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.r2.0.1.grch38,,,,mafdb.gnomad.r2.0.1.hs37d5,,,,mafdb.gnomad.r2.1.hs37d5,,,,mafdb.gnomadex.r2.0.1.grch38,,,,mafdb.gnomadex.r2.0.1.hs37d5,,,,mafdb.gnomadex.r2.1.hs37d5,,,,mafdb.topmed.freeze5.hg19,,,,mafdb.topmed.freeze5.hg38,,,,MCSEA,,,,MDTS,,,,一顿饭,,,,Medips,,,,甲基赫里西氏菌,,,,甲基分析,,,,甲基硫酸,,,,甲基赛克,,,,甲基菌,,,,最小值,,,,米拉,,,,mmdiff2,,,,马赛克,,,,Motifbreakr,,,,MotifMatchr,,,,mtseeker,,,,mtseekerdata,,,,多亚sayExexperiment,,,,多胎,,,,多希克科姆,,,,狭窄,,,,NORMR,,,,,,,,寡群,,,,omadb,,,,OpenPrimer,,,,有机体,,,,有机体,,,,校长,,,,panelcn.mops,,,,PBase,,,,PCAEXPLORER,,,,pepdat,,,,pepstat,,,,phastcons100way.ucsc.hg19,,,,phastcons100way.ucsc.hg38,,,,phastcons7way.ucsc.hg38,,,,pi,,,,图片,,,,PQSFINDER,,,,Prebs,,,,Primirtss,,,,probamr,,,,属属,,,,PVIZ,,,,杂种,,,,QDNASEQ,,,,qpgraph,,,,QPLEXANALYZER,,,,QSEA,,,,R3CPET,,,,R453plus1toolbox,,,,Rarevariantvis,,,,RCAS,,,,RCGH,,,,叙事,,,,recountworkflow,,,,区域人,,,,地区报告,,,,REMP,,,,repitools,,,,RGMQL,,,,肋骨蛋白,,,,rmmquant,,,,rnaprobr,,,,RNASEQMAP,,,,怒吼,,,,rtcgatoolbox,,,,Scmeth,,,,Scoreinvhap,,,,scpipe,,,,颈背,,,,seq2pathway,,,,Seqarray,,,,seqpattern,,,,seqplots,,,,seqsetvis,,,,seqsqc,,,,Seqvartools,,,,芝麻,,,,塞文,,,,Shortread,,,,签名者,,,,Simulatorz,,,,Snpchip,,,,snplocs.hsapiens.dbsnp.20101109,,,,snplocs.hsapiens.dbsnp.20120608,,,,snplocs.hsapiens.dbsnp141.grch38,,,,snplocs.hsapiens.dbsnp142.grch37,,,,snplocs.hsapiens.dbsnp144.grch37,,,,snplocs.hsapiens.dbsnp144.grch38,,,,snplocs.hsapiens.dbsnp149.grch38,,,,snplocs.hsapiens.dbsnp150.grch38,,,,snplocs.hsapiens.dbsnp151.grch38,,,,soggi,,,,somaticccanceralterations,,,,稀疏,,,,剪接图,,,,碎片,,,,Srnadiff,,,,斯坦,,,,Strandcheckr,,,,SVM2CRM,,,,Systempiper,,,,tcgabiolinks,,,,tcgautils,,,,tcgaworkflow,,,,TCSEQ,,,,tfarm,,,,TFBSTOOLS,,,,tfea.chip,,,,TFHAZ,,,,Titancna,,,,TrackTables,,,,transcriptr,,,,跨石,,,,特雷娜,,,,三元,,,,tsrchitect,,,,TVTB,,,,txreginfra,,,,独立,,,,变体滤波器,,,,VariantToolsData,,,,波动,,,,WigglePlotr,,,,xtrasnplocs.hsapiens.dbsnp141.grch38,,,,xtrasnplocs.hsapiens.dbsnp144.grch37,,,,xtrasnplocs.hsapiens.dbsnp144.grch38,,,,yrimulti
建议我 替代方案,,,,替代方案,,,,AnnotationHub,,,,Beadarrayusecases,,,,生物室,,,,生物基因,,,,生物比较,,,,芝加哥,,,,腹带,,,,epivizrchart,,,,GenomeInfodB,,,,geuvadistranscriptexpr,,,,glimma,,,,GSREG,,,,Gwastools,,,,HDF5Array,,,,InteractiveSplay,,,,iranges,,,,metaseqr,,,,幻影,,,,狭窄,,,,ngscopy,,,,OMICSPRINT,,,,Onassis,,,,RTCGA,,,,S4VECTORS,,,,seqgsea,,,,Sesamedata,,,,single.mtec.transcriptomes,,,,tfutils
链接到我
构建报告

包装档案

跟随2021年欧洲杯比分预测 在R会话中使用此软件包的说明。

源包 Genomicranges_1.34.0.tar.gz
Windows二进制 genomicranges_1.34.0.zip(32-和64位)
Mac OS X 10.11(El Capitan) Genomicranges_1.34.0.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.bioconductor.org:包装/基因组机器人
包装短URL //www.andersvercelli.com/packages/genomicranges/
软件包下载报告 下载统计

文档»

生物导体

r/克兰软件包和文档

支持»

请阅读发布指南。向以下位置之一发布有关生物导体的问题:

  • 支持网站- 有关生物处理套件的问题
  • Bioc-devel邮件列表 - 包装开发人员2021欧洲杯体育投注开户