Software for Computing and Annotating Genomic Ranges | Zendy

Michael Lawrence | Zendy; Wolfgang Huber | Zendy; Hervé Pagès | Zendy; Patrick Aboyoun | Zendy; Marc Carlson | Zendy; Robert Gentleman | Zendy; Martin Morgan | Zendy; Vincent J. Carey | Zendy

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Software for Computing and Annotating Genomic Ranges

Author(s) -

Michael Lawrence,

Wolfgang Huber,

Hervé Pagès,

Patrick Aboyoun,

Marc Carlson,

Robert Gentleman,

Martin Morgan,

Vincent J. Carey

Publication year - 2013

Publication title -

plos computational biology

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.628

H-Index - 182

eISSN - 1553-7358

pISSN - 1553-734X

DOI - 10.1371/journal.pcbi.1003118

Subject(s) - bioconductor , computer science , scalability , software , visualization , computational statistics , sequence alignment , data mining , genome , computational genomics , genomics , computational biology , biology , database , genetics , programming language , machine learning , gene , peptide sequence

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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