要安装此软件包,请启动R并输入:

##尝试http://如果不支持https:// url不支持源(“ //www.andersvercelli.com/bioclite.r”)bioclite(“ Genomicranges”)

在大多数情况下,您根本不需要下载包装存档。

基因组机

此软件包适用于生物导体的3.4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:3.4

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特性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准。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并输入:

##尝试http://如果不支持https:// url不支持源(“ //www.andersvercelli.com/bioclite.r”)bioclite(“ Genomicranges”)

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”)

PDF R脚本 您不知道的10件事(Bioc slide 2016)
PDF R脚本 快速介绍Granges和GrangeSlist对象(幻灯片)
PDF R脚本 基因组包装的简介
PDF R脚本 扩展基因组
PDF R脚本 基因组霍托斯
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 1.26.4
在生物导体中 Bioc 2.6(R-2.11)(7年)
执照 艺术2.0
要看 r(> = 2.10),方法,stats4,生物基因(> = 0.17.5),S4VECTORS(> = 0.9.47),iranges(> = 2.7.8),GenomeInfodB(> = 1.1.20)
进口 UTIT,统计,xvector
链接 S4VECTORS,,,,iranges
建议 生物酶,,,,AnnotationDbi(> = 1.21.1),注释,,,,生物弦(> = 2.25.3),rsamtools(> = 1.13.53),总结性特征(> = 0.1.5),矩阵,,,,基因组签名,,,,rtracklayer,,,,BSGENOME,,,,GenomicFeatures,,,,GVIZ,,,,变体,,,,AnnotationHub,,,,deseq2,,,,dexseq,,,,EDGER,,,,kegggraph,,,,生物使用,,,,消化,,,,运行,,,,bsgenome.hsapiens.ucsc.hg19,,,,BSGENOME.SCEREVISIAE.UCSC.SACCER2,,,,kegg.db,,,,HGU95AV2.DB,,,,org.hs.eg.db,,,,org.mm.eg.db,,,,org.sc.sgd.db,,,,帕西拉,,,,pasillabamsubset,,,,txdb.Athaliana.biomart.plantsmart22,,,,txdb.dmelanogaster.ucsc.dm3.ensgene,,,,txdb.hsapiens.ucsc.hg19,,,,bsgenome.mmusculus.ucsc.mm10,,,,txdb.mmusculus.ucsc.mm10.nowngene,,,,rnaseqdata.hnrnpc.bam.chr14,,,,HGU95AV2Probe
系统要求
增强
URL
取决于我 等位基因平衡,,,,Aneufinder,,,,Annmap,,,,AnnotationHubdata,,,,阿斯普利,,,,Baalchip,,,,basic4cseq,,,,BasicStarrseq,,,,贝塞克,,,,Biomvrcns,,,,Biseq,,,,bprmeth,,,,BSGENOME,,,,BSSEQ,,,,气泡,,,,Bumphunter,,,,咖啡店,,,,卡斯珀,,,,Champdata,,,,Cheung2010,,,,嵌合体,,,,芯片,,,,Chippeakanno,,,,chipqc,,,,chipseq,,,,chrogps,,,,Chromplot,,,,Chromstar,,,,Cindex,,,,清理,,,,CN. -ops,,,,cnpbayes,,,,CNVGSA,,,,cnvpanelizer,,,,Compepitools,,,,共识,,,,CSAR,,,,CSAW,,,,Deepsnv,,,,deseq2,,,,dexseq,,,,差异,,,,Diffhic,,,,DMRCALLER,,,,dmrcatedata,,,,dmrforpairs,,,,dnashaper,,,,doqtl,,,,Eatonetalchipseq,,,,富集图,,,,Ensembldb,,,,ememblvep,,,,Epgenomix,,,,外观复制,,,,fastseg,,,,FCCAC,,,,Fourcseq,,,,Funchip,,,,吉恩·布雷克(Genebreak),,,,代理商,,,,Genogam,,,,基因组签名,,,,GenomicFeatures,,,,Genomicfiles,,,,基因组菌,,,,Genoset,,,,geuvstore2,,,,GMAPR,,,,GMRP,,,,哥特,,,,Greylistchip,,,,grohmm,,,,Gtrellis,,,,Guideseq,,,,吉他,,,,GVIZ,,,,Helloranges,,,,Hiannotator,,,,Hilbertcurve,,,,HITC,,,,htseqtools,,,,IDEOVIZ,,,,inpas,,,,Intansv,,,,互动集,,,,Isomirs,,,,mbased,,,,metagene,,,,甲基分析,,,,甲基库,,,,甲基管,,,,Minfi,,,,突变模式,,,,Omiccircos,,,,PGA,,,,ping,,,,podkat,,,,,,,,R3CSEQ,,,,稀有,,,,rcade,,,,补偿,,,,区域人,,,,rfpred,,,,rgreat,,,,riboseqr,,,,Ripseeker,,,,rnbeads,,,,rnbeads.hg19,,,,rnbeads.hg38,,,,rnbeads.mm10,,,,rnbeads.mm9,,,,rnbeads.rn5,,,,rsamtools,,,,RSVSIM,,,,rtracklayer,,,,片段,,,,seqbias,,,,sgseq,,,,Sictools,,,,sigfuge,,,,Smite,,,,Snphood,,,,snplocs.hsapiens.dbsnp.20090506,,,,snplocs.hsapiens.dbsnp.20100427,,,,snplocs.hsapiens.dbsnp.20101109,,,,snplocs.hsapiens.dbsnp.20110815,,,,snplocs.hsapiens.dbsnp.2011119,,,,snplocs.hsapiens.dbsnp.20120608,,,,snplocs.hsapiens.dbsnp141.grch38,,,,snplocs.hsapiens.dbsnp142.grch37,,,,躯体签名,,,,总结性特征,,,,tarseqqc,,,,Titancna,,,,TrackViewer,,,,transview,,,,Traser,,,,香草,,,,变体,,,,变体工具,,,,vtpnet,,,,Wavcluster,,,,xtrasnplocs.hsapiens.dbsnp141.grch38,,,,yapsa,,,,yrimulti
进口我 ALDEX2,,,,高山,,,,Annotatr,,,,arrayexpresshts,,,,不良区域,,,,舞会礼服,,,,bamsignals,,,,BBCANALYZER,,,,Beadarray,,,,,,,,Biovizbase,,,,Biseq,,,,BSGENOME,,,,卡格,,,,cexor,,,,CGDV17,,,,冠军,,,,Chipenrich,,,,chipenrich.data,,,,Chipseeker,,,,chipseq,,,,chipseqr,,,,ChromDraw,,,,ChromheatMap,,,,CNER,,,,cnpbayes,,,,彗星,,,,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,,,,Drimseq,,,,EasyRnaseq,,,,EDASEQ,,,,埃尔默,,,,Elmer.Data,,,,epivizr,,,,epivizrdata,,,,Erma,,,,FitCons.UCSC.HG19,,,,拖鞋,,,,Fourcseq,,,,funcisnp,,,,GenBankr,,,,基因贡献,,,,Genegeneinter,,,,基因组化,,,,基因组合,,,,基因组签名,,,,基因组间,,,,Genotypeeval,,,,Genvisr,,,,GGBASE,,,,GGBIO,,,,ggtools,,,,GoogleGenomics,,,,GQTLBASE,,,,gqtlstats,,,,Gwascat,,,,H5VC,,,,Hireadsprocessor,,,,htseqgenie,,,,检查,,,,IVAS,,,,接口,,,,Leebamviews,,,,萝拉,,,,Lumi,,,,M3D,,,,Madseq,,,,mafdb.1kgenomes.phase1.hs37d5,,,,mafdb.1kgenomes.phase3.hs37d5,,,,mafdb.esp6500si.v2.ssa137,,,,mafdb.esp6500si.v2.ssa137.grch38,,,,mafdb.esp6500si.v2.ssa137.hs37d5,,,,mafdb.exac.r0.3.1.nontcga.snvs.hs37d5,,,,mafdb.exac.r0.3.1.snvs.hs37d5,,,,一顿饭,,,,Medips,,,,甲基分析,,,,甲基赛克,,,,甲基菌,,,,最小值,,,,mmdiff2,,,,马赛克,,,,Motifbreakr,,,,多亚sayExexperiment,,,,多胎,,,,狭窄,,,,NORMR,,,,,,,,寡群,,,,有机体,,,,PBase,,,,PCAEXPLORER,,,,pepdat,,,,pepstat,,,,phastcons100way.ucsc.hg19,,,,phastcons100way.ucsc.hg38,,,,phastcons7way.ucsc.hg38,,,,pi,,,,图片,,,,PQSFINDER,,,,Prebs,,,,probamr,,,,属属,,,,PVIZ,,,,杂种,,,,QDNASEQ,,,,qpgraph,,,,QSEA,,,,R3CPET,,,,R453plus1toolbox,,,,Rarevariantvis,,,,RCAS,,,,RCGH,,,,叙事,,,,区域人,,,,地区报告,,,,repitools,,,,肋骨蛋白,,,,rnaprobr,,,,RNASEQMAP,,,,怒吼,,,,seq2pathway,,,,Seqarray,,,,seqpattern,,,,seqplots,,,,Seqvartools,,,,Shortread,,,,签名者,,,,Simulatorz,,,,Snpchip,,,,snplocs.hsapiens.dbsnp.20090506,,,,snplocs.hsapiens.dbsnp.20100427,,,,snplocs.hsapiens.dbsnp.20101109,,,,snplocs.hsapiens.dbsnp.20110815,,,,snplocs.hsapiens.dbsnp.2011119,,,,snplocs.hsapiens.dbsnp.20120608,,,,snplocs.hsapiens.dbsnp141.grch38,,,,snplocs.hsapiens.dbsnp142.grch37,,,,snplocs.hsapiens.dbsnp144.grch37,,,,snplocs.hsapiens.dbsnp144.grch38,,,,soggi,,,,somaticccanceralterations,,,,拼接器,,,,剪接图,,,,碎片,,,,斯坦,,,,SVM2CRM,,,,Systempiper,,,,tcgabiolinks,,,,TFBSTOOLS,,,,TrackTables,,,,transcriptr,,,,三元,,,,TVTB,,,,变体滤波器,,,,波动,,,,xtrasnplocs.hsapiens.dbsnp141.grch38,,,,xtrasnplocs.hsapiens.dbsnp144.grch37,,,,xtrasnplocs.hsapiens.dbsnp144.grch38
建议我 替代方案,,,,AnnotationHub,,,,Beadarrayusecases,,,,生物室,,,,生物基因,,,,生物比较,,,,芝加哥,,,,腹带,,,,GenomeInfodB,,,,geuvadistranscriptexpr,,,,HDF5Array,,,,InteractiveSplay,,,,iranges,,,,metaseqr,,,,幻影,,,,狭窄,,,,ngscopy,,,,RTCGA,,,,S4VECTORS,,,,seqgsea,,,,single.mtec.transcriptomes
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。

包源 genomicranges_1.26.4.tar.gz
Windows二进制 genomicranges_1.26.4.zip(32-和64位)
Mac OS X 10.9(Mavericks) Genomicranges_1.26.4.tgz
颠覆源 (用户名/密码:ReadOnly)
git源 https://github.com/bioconductor-mirror/genomicranges/tree/release-3.4
包装短URL //www.andersvercelli.com/packages/genomicranges/
软件包下载报告 下载统计

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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
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