The R-based Bioconductor open source software project has released Bioconductor version 2.3.
This release includes 36 new software packages, and many changes to existing packages. Bioconductor 2.3 comprises a total of 294 software packages and is compatible with the recently released R 2.8.0.
This release contains a septet of packages: BSgenome, Biostrings, ShortRead, IRanges, HilbertVis, HilbertVisGUI, and rtracklayer that are suited to analyze second-generation high-throughput DNA sequence data.
R 2.8.0 uses a new Mac OS X binary package distribution system for which the CRAN and BioC repositories must be adapted.
The BSgenome package provides the backbone for representing genome sequences from many different organisms including human, mouse, rat, dog, chimp, chicken, cow, fruit fly, honey bee, yeast, E. coli, C. elegans, and Arabidopsis. The Biostrings package performs fast or flexible alignments between reads and genomes. The ShortRead package provides tools for importation/exportation and quality assurance of common data formats.
The IRanges package offers an emerging infrastructure for managing very large data objects and for range-based data representation. The packages HilbertVis and HilbertVisGUI display data with space-filling curves that maintain the spatial information implied by the linearity of chromosomes. The rtracklayer package provides an interface to genome browsers and their annotation tracks.