"He who passively accepts evil is as much involved in it as he who helps to perpetrate it" - Martin Luther King, Jr.
2013 August: Updated snpMatrix 4-digit series and Bioconductor snpStats Bugs. snpMatrix 184.108.40.206 was released in June with performance improvements to the VCF related code.
2013 April Update:snpMatrix 220.127.116.11 introduces the capability of processing VCF files, especially those from the 1000 Genome Project. A new vignette, I/O Suite, VCF (1000 Genome) and HapMap, serves as the tutorial and test suite for the new functionality. There is a new uncertain= option for reading Chiamo data; and leading up to it, fixed another bug in Bioconductor snpStats.
2013 April Update: snpMatrix 4-digit series describes the enhancements/changes not in the 3-digit versions. Bioconductor snpStats Bugs have also been updated.
2012 March Update: There is a whole bunch of Mac OS X builds: CelQuantileNorm, vcftools, samtools, tabix at the moment, more to follow. They are fat binaries (i.e. works on both PowerPC and Intel 32-bit/64-bit Macs) ; snpStats 1.5.5 turned out to be "differently buggy" so there is a snpStats 18.104.22.168, which is also the first R package available as an Mac OS X build. See link above for installation instructions. Bioconductor snpStats Bugs continues to track the HEAD of snpStats development, while Bioconductor snpStats Bugs 1.5.4, Bioconductor snpStats Bugs 1.3.6 tracks the differently buggy ones.
2012 January Update: snpStats - unsupported, less buggy at top level; added less buggy snpStats 22.214.171.124 and 126.96.36.199 . Windows and Android ports of vcftools, tabix, samtools. New Mono 188.8.131.52 linux and windows builds. New "Algorithms and Thailand" vignette, "Tutorial 2007" (File I/O testsuite) vignette. Some new files housed elsewhere at http://htl10.users.sourceforge.net/Languages/. Both Bioconductor snpStats Bugs and Bioconductor snpStats Bugs were updated.
2011 October Update: The "snpStats Bugs" vignette cataloging bugs on Bioc version of snpMatrix and snpStats have been substantially updated, and split into two: current snpStats Bugs and snpStats Bugs 1.3.6 (up to 20th October 2011). Look under file releases for possibly more up-to-date versions of these.
2011 September Update: Illumina Bead Pool Manifest support in both Broccoli and snpMatrix; new "snpStats Bug" vignette, "Regression and Migration" vignette in snpMatrix: all past and present users of either should check their 2-df genotypic results.
2011 August Update: Adding reference to the Android port of the BeanSprout suite. EGT support added to snpMatrix.
2011 May Addition: Animation for Bioinformatics Talk May 2011