High-throughput sequence analysis
Key packages
A work flow might involve the following packages, all available in the release version of Bioconductor
- ShortRead for file I/O, quality assessment, and high-level, general purpose data summary.
- Biostrings for alignment, pattern matching (e.g., primer removal), and data manipulation of large biological sequences or sets of sequences. There are a series of pre-built BSgenome.* sequence annotation packages.
- BSgenome for accessing and manipulating curated whole-genome representations.
- rtracklayer for import and export of tracks to browsers like the UCSC genome browser.
- IRanges and genomeIntervals for range-based (e.g., chromosomal regions) calculation, data manipulation, and general-purpose data representation.
Packages are installed using biocLite(). These packages are under active development; those on the cutting edge might wish to use the development version of R, and hence the development version of the packages listed above. In addition, the chipseq package is available (as of 8 May 2009) using subversion.
Packages have extensive help pages, and include vignettes highlighting common use cases; the help pages and vignettes are available from within R (e.g., ?DNAStringSet) and on the pages linked above.