WhopGenome: High-speed processing of whole-genome VCF-format variation data, FASTA-format sequence data and several alignments formats

WhopGenome's provides very fast access to whole genome, population scale variation data from VCF files and sequence data from FASTA-formatted files. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.

Version: 0.8.2
Depends: R (≥ 1.8.0)
Suggests: RMySQL, DBI, AnnotationDbi
Published: 2013-12-03
Author: Ulrich Wittelsbuerger
Maintainer: Ulrich Wittelsbuerger <ulrich.wittelsbuerger at uni-duesseldorf.de>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Copyright: This package uses zlib, Tabix, bgzf and faidx. Zlib by Jean-loup Gally <jloup@gzip.org> and Mark Adler <madler@alumni.caltech.edu>, uses the Zlib licence. Tabix and FaIdx by Heng Li <lh3@live.co.uk> use the MIT licence. BGZF as by Bob Handsaker and modified by Heng Li uses the MIT licence. Anything else was written entirely by Ulrich Wittelsbuerger. All third-party code has been slightly modified to conform to R package development requirements such as removal or replacement of printf, fprintf on stderr and functions that would terminate a running R session by R-supplied equivalents as well as modifications that eliminate most compiler warnings.
NeedsCompilation: yes
CRAN checks: WhopGenome results

Downloads:

Reference manual: WhopGenome.pdf
Package source: WhopGenome_0.8.2.tar.gz
Windows binaries: r-devel: WhopGenome_0.8.2.zip, r-release: WhopGenome_0.8.2.zip, r-oldrel: WhopGenome_0.8.2.zip
OS X Snow Leopard binaries: r-release: WhopGenome_0.8.2.tgz, r-oldrel: WhopGenome_0.8.2.tgz
OS X Mavericks binaries: r-release: WhopGenome_0.8.2.tgz
Old sources: WhopGenome archive

Reverse dependencies:

Reverse suggests: PopGenome