Software for Computing and Annotating Genomic Ranges

被引：2646

作者：

Lawrence, Michael ^{[1
]}

Huber, Wolfgang ^{[2
,3
]}

Pages, Herve ^{[4
]}

Aboyoun, Patrick ^{[4
]}

Carlson, Marc ^{[4
]}

Gentleman, Robert ^{[1
]}

Morgan, Martin T. ^{[4
]}

Carey, Vincent J. ^{[5
]}

机构：

[1] Genentech Inc, Bioinformat & Computat Biol, San Francisco, CA 94080 USA

[2] European Mol Biol Lab, Genome Biol Unit, D-69012 Heidelberg, Germany

[3] European Bioinformat Inst, Cambridge, England

[4] Fred Hutchinson Canc Res Ctr, Seattle, WA 98104 USA

[5] Harvard Univ, Brigham & Womens Hosp, Sch Med, Channing Div Network Med, Boston, MA 02115 USA

来源：

PLOS COMPUTATIONAL BIOLOGY | 2013年 / 9卷 / 08期

基金：

美国国家卫生研究院;

关键词：

BIOCONDUCTOR; PACKAGE;

D O I：

10.1371/journal.pcbi.1003118

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

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