rtracklayer

doi:10.18129/b9.bioc.rtracklayer

R接口到基因组注释文件和UCSC基因组浏览器

生物导体版本:版本(3.15)

可扩展与多个基因组浏览器(目前内置UCSC)交互的框架,并以各种格式(目前GFF,BED,BEDGRAPH,BEDGRAPH,BED15,WIG,WIG,BIGWIG和2位内置)操纵注释轨道。用户可以向/从受支持的浏览器导出/导入跟踪,以及查询并修改浏览器状态,例如当前视口。

作者:迈克尔·劳伦斯,文斯·凯里,罗伯特·绅士

维护者:迈克尔·劳伦斯(Michael Lawrence)

引用(从r内,输入引用(“ rtracklayer”)):

安装

要安装此软件包,请启动R(版本“ 4.2”)并输入:

if(!quired(“ Biocmanager”,悄悄= true))install.packages(“ Biocmanager”)Biocmanager :: install(“ rtracklayer”)

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(“ rtracklayer”)

PDF R脚本 rtracklayer
PDF 参考手册
文本 消息
文本 安装
文本 执照

细节

生物浏览 注解,,,,DataImport,,,,软件,,,,可视化
版本 1.56.1
在生物导体中 Bioc 2.2(R-2.7)(14年)
执照 Artistic-2.0 +文件执照
要看 r(> = 3.5.0),方法,基因组机(> = 1.37.2)
进口 XML(> = 1.98-0),生物基因(> = 0.35.3),S4VECTORS(> = 0.23.18),iranges(> = 2.13.13),xvector(> = 0.19.7),GenomeInfodB(> = 1.15.2),生物弦(> = 2.47.6),Zlibbioc,,,,rcurl(> = 1.4-2),rsamtools(> = 1.31.2),基因组签名(> = 1.15.6),Biocio, 工具,Restfulr(> = 0.0.13)
链接 S4VECTORS,,,,iranges,,,,xvector
建议 BSGENOME(> = 1.33.4),人类系统,,,,microRNA(> = 1.1.1),GeneFilter,,,,林玛,,,,org.hs.eg.db,,,,hgu133plus2.db,,,,GenomicFeatures,,,,bsgenome.hsapiens.ucsc.hg19,,,,txdb.hsapiens.ucsc.hg19,,,,运行
系统要求
增强
URL
取决于我 Brgenomics,,,,BSGENOME,,,,Cagefightr,,,,芯片,,,,CoverageView,,,,CSSQ,,,,腹带,,,,Eatonetalchipseq,,,,DEBLUSTER,,,,Genextender,,,,Genomicfiles,,,,grohmm,,,,吉他,,,,Helloranges,,,,IDEOVIZ,,,,举起,,,,甲基赛克,,,,Orfhunter,,,,R3CSEQ,,,,测序,,,,结构视频隔离,,,,Svanumt,,,,Svaretro
进口我 AnnotationHubdata,,,,Annotatr,,,,apalyzer,,,,Aspediafi,,,,atacseqqc,,,,舞会礼服,,,,BGEECALL,,,,BindingsIteFinder,,,,饼干,,,,Biseq,,,,分支机构,,,,BSGENOME,,,,卡格,,,,卡斯珀,,,,cexor,,,,chipanalyser,,,,Chipenrich,,,,chipenrich.data,,,,Chippeakanno,,,,Chipseeker,,,,ChromheatMap,,,,染色体,,,,Chromswitch,,,,Circrnaprofiler,,,,夹层,,,,CNER,,,,彗星,,,,carpartmap,,,,共识,,,,contibait,,,,Conumee,,,,CustomProdb,,,,达斯珀,,,,深布鲁尔,,,,德芬德,,,,DESCAN2,,,,Diffhic,,,,diffloop,,,,diffutr,,,,DMCFB,,,,dmchmm,,,,dmrcatedata,,,,DMRSEQ,,,,埃尔默,,,,EnhancerHomogsearch,,,,富集,,,,Ensembldb,,,,Epicompare,,,,epideCoder,,,,Epigrahmm,,,,Erma,,,,esatac,,,,Exomepeak2,,,,伸出,,,,fcscan,,,,Findit2,,,,火焰,,,,GenBankr,,,,基因贡献,,,,Genelendatabase,,,,GenStructurotootools,,,,基因组化,,,,GenomicFeatures,,,,基因组间,,,,基因组态,,,,Genotypeeval,,,,GGBIO,,,,GMAPR,,,,Gmoviz,,,,哥特,,,,Greylistchip,,,,GVIZ,,,,Hiannotator,,,,hicdcplus,,,,HITC,,,,htseqgenie,,,,冰茶,,,,IGVR,,,,检查,,,,intad,,,,同工型间分析仪,,,,核粒子,,,,M6aboost,,,,Macpet,,,,Madseq,,,,马瑟,,,,Medips,,,,metagene,,,,metagene2,,,,metaseqr2,,,,Methrix,,,,甲基库,,,,Motifbreakr,,,,主题,,,,Multicrispr,,,,mungesumstats,,,,NADFINDER,,,,附近,,,,诺斯,,,,NORMR,,,,nxtirfcore,,,,nxtirfdata,,,,奥德,,,,OGRE,,,,OMICSPCA,,,,ORFIK,,,,过去的,,,,周期性,,,,plyranges,,,,婴儿车,,,,Primirtss,,,,probamr,,,,profileplyr,,,,属属,,,,QSEA,,,,,,,,RCAS,,,,叙事,,,,ROCOUT3,,,,补偿,,,,区域人,,,,REMP,,,,repitools,,,,RGMQL,,,,肋骨蛋白,,,,RibosomeProfilingQC,,,,Rifi,,,,ripat,,,,rlseq,,,,RMSPC,,,,rnamodr,,,,怒吼,,,,Scanmirapp,,,,Scanvis,,,,scdblfinder,,,,scpipe,,,,颈背,,,,seqcat,,,,seqsetvis,,,,塞文,,,,sgseq,,,,Shinyepico,,,,sigspack,,,,singscoreamlmutations,,,,Sitadela,,,,soggi,,,,空间Libd,,,,Srnadiff,,,,TFBSTOOLS,,,,TrackViewer,,,,transcriptr,,,,Tress,,,,Trnascanimport,,,,tsrchitect,,,,txcutr,,,,变体,,,,变体工具,,,,Wavcluster,,,,WigglePlotr
建议我 高山,,,,AnnotationHub,,,,自治,,,,Biocfilecache,,,,Biovizbase,,,,BSSEQ,,,,chipseqdb,,,,西塞罗,,,,Cindex,,,,Compepitools,,,,crisprvariants,,,,damefinder,,,,艾萨尔,,,,日期,,,,Epistack,,,,epitxdb.hs.hg38,,,,epitxdb.sc.saccer3,,,,epivizrchart,,,,epivizrdata,,,,fdb.fantom4.promoters.hg19,,,,Genextender,,,,基因组签名,,,,基因组分布,,,,GenomicInteractionNodes,,,,基因组机,,,,geuvadistranscriptexpr,,,,Goseq,,,,Gwascat,,,,inpas,,,,InteractiveSplay,,,,Megadepth,,,,甲基菌,,,,Mirbaseconverter,,,,突变模式,,,,纳米管,,,,有机体,,,,pasillatranscriptexpr,,,,pi,,,,图片,,,,ping,,,,管框,,,,Plotgardener,,,,PQSFINDER,,,,Proteodisco,,,,R453plus1toolbox,,,,rcistarget,,,,rgadem,,,,林戈,,,,rnamodr.alkanilineseq,,,,rnamodr.ml,,,,rnamodr.ribomethseq,,,,rnbeads,,,,RSVSIM,,,,签名者,,,,相似,,,,Synextend,,,,Systempiper,,,,SystemPiperData,,,,TAPSEQ,,,,tcgautils,,,,三元,,,,Trnadbimport,,,,TVTB,,,,xcore
链接到我
构建报告

包装档案

跟随bob 体育网址 在R会话中使用此软件包的说明。

源包 rtracklayer_1.56.1.tar.gz
Windows二进制 rtracklayer_1.56.1.zip
MacOS 10.13(高山脉) rtracklayer_1.56.1.tgz
源存储库 git克隆https://git.bioconductor.org/packages/rtracklayer
源存储库(开发人员访问) git clone git@git.bioconductor.org:packages/rtracklayer
包装短URL //www.anjoumacpherson.com/packages/rtracklayer/
软件包下载报告 下载统计
Bioc 3.15的旧源软件包 来源存档

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