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Software for Computing and Annotating Genomic Ranges

Overview
Journal PLoS Comput Biol
Specialty Biology
Date 2013 Aug 17
PMID 23950696
Citations 2149
Authors
Michael Lawrence
Wolfgang Huber
Herve Pages
Patrick Aboyoun
Marc Carlson
Robert Gentleman
Martin T Morgan
Vincent J Carey
Affiliations
Soon will be listed here.
Abstract

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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