GenomicRanges

DOI:10.18129 / B9.bioc.GenomicRanges

基因组间隔的表示和操作

Bioconductor版本:发行版(3.13)

在分析高通量测序数据(又称NGS数据)时,有效地表示和操作基因组注释和比对的能力发挥着核心作用。GenomicRanges包定义了通用容器,用于存储和操作基因组间隔和基因组定义的变量。更专门的容器分别定义在GenomicAlignments和summarizeexperiment包中,用于表示和操作针对参考基因组的短对齐,或类似矩阵的实验摘要。这两个软件包都建立在GenomicRanges基础设施之上。

作者:P. Aboyoun, H. Pagès, M. Lawrence

维护者:Bioconductor Package维护者< Maintainer at Bioconductor .org>

引文(从R内,输入引用(“GenomicRanges”)):

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")::install("GenomicRanges")

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(“GenomicRanges”)

超文本标记语言 R脚本 1.genome ranges软件包简介
PDF R脚本 2.GenomicRanges howto
PDF R脚本 3.GRanges和GRangesList对象的简要介绍(幻灯片)
PDF R脚本 4.你不知道的十件事(幻灯片来自bio2016)
PDF R脚本 5.延长GenomicRanges
PDF 参考手册
文本 新闻

细节

biocViews 注释报道DataRepresentation遗传学GenomeAnnotation基础设施测序软件
版本 1.44.0
在Bioconductor BioC 2.6 (R-2.11)(11年)
许可证 艺术- 2.0
取决于 R(>= 4.0.0),方法,stats4,BiocGenerics(> = 0.37.0),S4Vectors(> = 0.27.12),IRanges(> = 2.23.9),GenomeInfoDb(> = 1.15.2)
进口 跑龙套,统计数据,XVector(> = 0.29.2)
链接 S4VectorsIRanges
建议 矩阵BiobaseAnnotationDbi注释Biostrings(> = 2.25.3),SummarizedExperiment(> = 0.1.5),Rsamtools(> = 1.13.53),GenomicAlignmentsrtracklayerBSgenomeGenomicFeaturesGvizVariantAnnotationAnnotationHubDESeq2DEXSeq刨边机KEGGgraphRNAseqData.HNRNPC.bam.chr14pasillaBamSubsetKEGGRESThgu95av2.dbhgu95av2probeBSgenome.Scerevisiae.UCSC.sacCer2BSgenome.Hsapiens.UCSC.hg19BSgenome.Mmusculus.UCSC.mm10TxDb.Athaliana.BioMart.plantsmart22TxDb.Dmelanogaster.UCSC.dm3.ensGeneTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Mmusculus.UCSC.mm10.knownGeneRUnit消化knitrrmarkdownBiocStyle
SystemRequirements
增强了
URL //www.anjoumacpherson.com/packages/GenomicRanges
BugReports https://github.com/Bioconductor/GenomicRanges/issues
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建议我 alternativeSplicingEvents.hg19alternativeSplicingEvents.hg38AnnotationHub自治BeadArrayUseCasesbiobroomBiocGenericsBiocParallelCAGEWorkflow芝加哥CNVgearsComplexHeatmap腰带epivizrChartGenomeInfoDbGenomicStateGeuvadisTranscriptExprGlimmaGSRegGWASToolsHDF5ArrayInteractiveComplexHeatmapinteractiveDisplayIRangesmaftools海市蜃楼纳米管omicsPrint奥纳西斯parglmsrecountmethylationRNAmodR。数据RTCGAS4VectorsSeqGSEAsesameDataSingle.mTEC.Transcriptomes飞溅TFutilsuniversalmotif
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包档案

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源包 GenomicRanges_1.44.0.tar.gz
Windows二进制 GenomicRanges_1.44.0.zip
macOS 10.13 (High Sierra) GenomicRanges_1.44.0.tgz
源库 git克隆https://git.bioconductor.org/packages/GenomicRanges
源存储库(开发人员访问) git克隆git@git.bioconductor.org:packages/GenomicRanges
包短Url //www.anjoumacpherson.com/packages/GenomicRanges/
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