rtracklayer
DOI:
10.18129 / B9.bioc.rtracklayer
此包适用于Bioconductor 3.13版;有关稳定的最新发布版本,请参见rtracklayer.
R界面到基因组注释文件和UCSC基因组浏览器
Bioconductor版本:3.13
可扩展的框架,用于与多个基因组浏览器交互(目前内置UCSC),并以各种格式操作注释轨道(目前内置GFF、BED、bedGraph、BED15、WIG、BigWig和2bit)。用户可以从受支持的浏览器中导出/导入曲目,以及查询和修改浏览器状态,例如当前的视口。
作者:迈克尔·劳伦斯,文斯·凯里,罗伯特·绅士
维护者:Michael Lawrence
引文(从R内,输入引用(“rtracklayer”)
):
安装
要安装此包,请启动R(版本“4.1”)并输入:
如果(!requireNamespace("BiocManager", quiet = TRUE)) install.packages("BiocManager")
对于R的旧版本,请参考相应的Bioconductor释放.
文档
要查看系统中安装的此包版本的文档,请启动R并输入:
browseVignettes(“rtracklayer”)
细节
biocViews |
注释,DataImport,软件,可视化 |
版本 |
1.52.1 |
在Bioconductor |
BioC 2.2 (R-2.7)(13.5年) |
许可证 |
art -2.0 +文件许可证 |
取决于 |
R(>= 3.3),方法,GenomicRanges(> = 1.37.2) |
进口 |
XML(1.98 > = 0),BiocGenerics(> = 0.35.3),S4Vectors(> = 0.23.18),IRanges(> = 2.13.13),XVector(> = 0.19.7),GenomeInfoDb(> = 1.15.2),Biostrings(> = 2.47.6),zlibbioc,RCurl(> = 1.4 2),Rsamtools(> = 1.31.2),GenomicAlignments(> = 1.15.6),BiocIO、工具、restfulr(> = 0.0.13) |
链接 |
S4Vectors,IRanges,XVector |
建议 |
BSgenome(> = 1.33.4),humanStemCell,微(> = 1.1.1),genefilter,limma,org.Hs.eg.db,hgu133plus2.db,GenomicFeatures,BSgenome.Hsapiens.UCSC.hg19,TxDb.Hsapiens.UCSC.hg19.knownGene,RUnit |
SystemRequirements |
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增强了 |
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URL |
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全靠我 |
BRGenomics,BSgenome,CAGEfightR,ChIPComp,ChIPSeqSpike,CoverageView,CSSQ,腰带,EatonEtAlChIPseq,ExCluster,geneXtendeR,GenomicFiles,groHMM,吉他,HelloRanges,IdeoViz,liftOver,MethylSeekR,ORFhunteR,r3Cseq,测序,StructuralVariantAnnotation |
进口我 |
阿尔卑斯山脉,AnnotationHubData,annotatr,APAlyzer,ASpediaFI,ATACseqQC,舞会礼服,BgeeCall,biscuiteer,BiSeq,分歧点,BSgenome,篮球选手,卡斯珀,CexoR,ChIPanalyser,chipenrich,chipenrich.data,ChIPpeakAnno,ChIPseeker,ChromHeatMap,ChromSCape,chromswitch,circRNAprofiler,cn,彗星,compartmap,CompGO,consensusSeekeR,contiBAIT,conumee,customProDB,位深蓝,derfinder,DEScan2,diffHic,diffloop,diffUTR,DMCFB,DMCHMM,DMRcatedata,dmrseq,埃尔默,ENCODExplorer,enrichTF,ensembldb,epidecodeR,epigraHMM,erma,esATAC,exomePeak2,fcScan,genbankr,geneAttribution,geneLenDataBase,GeneStructureTools,genomation,GenomicFeatures,GenomicInteractions,GenomicState,genotypeeval,ggbio,gmapR,gmoviz,哥特,GreyListChIP,Gviz,hiAnnotator,HiCDCPlus,HiTC,HTSeqGenie,icetea,igvR,检查,InTAD,IsoformSwitchAnalyzeR,karyoploteR,MACPET,MADSEQ,微波激射器,MEDIPS,metagene,metagene2,metaseqR2,methrix,methyAnalysis,methylKit,motifbreakR,MotifDb,multicrispr,NADfinder,nanotatoR,nearBynding,NoRCE,normr,OMICsPCA,ORFik,过去的,periodicDNA,plyranges,婴儿车,primirTSS,proBAMr,profileplyr,PureCN,qsea,QuasR,美国广播公司,重新计票,recount3,收回,地区,REMP,Repitools,RGMQL,RiboProfiling,ribosomeProfilingQC,RIPAT,RNAmodR,RNAprobR,咆哮,SCANVIS,scPipe,颈背,seqCAT,seqplots,seqsetvis,sevenC,SGSeq,shinyepico,SigsPack,SingscoreAMLMutations,sitadela,soGGi,srnadiff,systemPipeRdata,TFBSTools,trackViewer,transcriptR,tRNAscanImport,TSRchitect,VariantAnnotation,VariantTools,wavClusteR,wiggleplotr |
建议我 |
高山,AnnotationHub,自治,BiocFileCache,biovizBase,bsseq,chipseqDB,西塞罗,CINdex,compEpiTools,CrispRVariants,DAMEfinder,dasper,dsQTL,eisaR,EpiTxDb.Hs.hg38,EpiTxDb.Sc.sacCer3,epivizrChart,epivizrData,FDb.FANTOM4.promoters.hg19,geneXtendeR,GenomicAlignments,GenomicDistributions,GenomicRanges,GeuvadisTranscriptExpr,goseq,gwascat,InPAS,interactiveDisplay,megadepth,methylumi,miRBaseConverter,MutationalPatterns,纳米管,OrganismDbi,PasillaTranscriptExpr,π,图片,平,pipeFrame,pqsfinder,R453Plus1Toolbox,RcisTarget,rGADEM,林格,RNAmodR。AlkAnilineSeq,RNAmodR。毫升,RNAmodR。RiboMethSeq,RnBeads,RSVSim,签名者,similaRpeak,spatialLIBD,SynExtend,TAPseq,TCGAutils,三层,tRNAdbImport,TVTB |
链接到我 |
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构建报告 |
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包档案
遵循bob 体育网址
在R会话中使用此包的说明。