Introduction

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.

Publications

  1. Software for computing and annotating genomic ranges.
    Cite this
    Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ, 2013-01-01 - PLoS computational biology

Credits

  1. Michael Lawrence
    Developer

    Bioinformatics and Computational Biology, Genentech

  2. Wolfgang Huber
    Developer

  3. Hervé Pagès
    Developer

  4. Patrick Aboyoun
    Developer

  5. Marc Carlson
    Developer

  6. Robert Gentleman
    Developer

  7. Martin T Morgan
    Developer

  8. Vincent J Carey
    Investigator

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Summary
AccessionBT000319
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByVincent J Carey