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

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 pa...