Software for computing and annotating genomic ranges

• Published in: PLoS computational biology Vol. 9; no. 8; p. e1003118
• Main Authors: Lawrence, Michael, Huber, Wolfgang, Pagès, Hervé, Aboyoun, Patrick, Carlson, Marc, Gentleman, Robert, Morgan, Martin T, Carey, Vincent J
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.08.2013; Public Library of Science (PLoS)
• Subjects: Algorithms; Animals; Application programming interface; Behavior; Binding sites; Biology; Computational biology; Computer Science; Databases, Genetic; Gene expression; Genomes; Genomics; Genomics - methods; Genomics - standards; Humans; Infrastructure; Metadata; Mice; Sequence Alignment; Sequence Analysis, DNA; Software; Studies; Technology application; United States; Sequence Alignment; Algorithms; Animals; Genomics; Humans; Databases, Genetic; Mice; Software; Sequence Analysis, DNA
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1003118

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.