Software Used at the Workshop

PLINK http://pngu.mgh.harvard.edu/~purcell/plink/
PLINK/SEQ http://atgu.mgh.harvard.edu/plinkseq/
Haploview http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview
gcta http://www.complextraitgenomics.com/software/gcta/
minimac http://genome.sph.umich.edu/wiki/Minimac
mach http://genome.sph.umich.edu/wiki/MaCH
GotCloud http://genome.sph.umich.edu/wiki/GotCloud
EPACTS http://genome.sph.umich.edu/wiki/EPACTS
merlin http://www.sph.umich.edu/csg/abecasis/Merlin/
qtdt http://www.sph.umich.edu/csg/abecasis/QTDT/
Rare-Metal http://genome.sph.umich.edu/wiki/Rare-Metal
Rare-Metal-Worker http://genome.sph.umich.edu/wiki/Rare-Metal-Worker
JAG http://ctglab.nl/software/
Jamp http://ctglab.nl/software/
tates http://ctglab.nl/software/
sgene http://ibg.colorado.edu/dokuwiki/lib/exe/fetch.php?media=workshop:2009:sgene.exe
KGG http://bioinfo.hku.hk/kggweb/
KGGSeq http://statgenpro.psychiatry.hku.hk/kggseq/
pspp http://www.gnu.org/software/pspp/
PennCNV http://www.openbioinformatics.org/penncnv/
xhmm http://atgu.mgh.harvard.edu/xhmm/
eigenstrat http://genepath.med.harvard.edu/~reich/Software.htm
BayeScan http://cmpg.unibe.ch/software/bayescan/
R http://cran.us.r-project.org/
- OpenMx http://openmx.psyc.virginia.edu/
- R-MASS http://cran.r-project.org/web/packages/MASS/index.html
- R-psych http://cran.r-project.org/web/packages/psych/
- R-car http://cran.r-project.org/web/packages/car/
- R-sem http://cran.r-project.org/web/packages/sem/
- Rplinkseq http://atgu.mgh.harvard.edu/plinkseq/r-intro.shtml
- Rstudio http://www.rstudio.com/