Software available for download
HapSample is a web
application for
simulating SNP genotypes for case-control and affected-child trio studies by
resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs
to be "genotyped," along with a disease model file that describes causal SNPs
and their effect sizes. The simulation tool is appropriate for candidate
regions or whole-genome scans. A command line version is also available
here .
Bias correction in genome scans. R code
and an Excel calculator are available
here . The paper
can be downloaded here .
The software,
ShrunkenPCA,
implements the shrunken principal component analysis that automatically
accounts for genomic correlation structure among SNPs.
ShrunkenPCA is compatible with the most popular stratification analysis
tool,
EigenSoft .
Nonparametric Bayesian method for mapping gene-gene interaction. The
manuscript can be downloaded here . So is the
software . You may test the
method by running the sample perl code located in "test" folder.
Semiparametric multiple QTL mapping method where
the non-genetic covariate effects are modeled
nonparametrically.
The software and the related paper
can be downloaded. Detailed user manual will be posted soon.
The software on Bayesian QTL mapping for RIX data can be downloaded
here .
The software on RNA-seq analysis of F1 reciprocal crosses can be downloaded
here .
The software for fast eQTL analysis of twin data can be downloaded
here .