Software available for download
<li> <a href="http://www.hapsample.org"> HapSample </a> 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
<a href="http://bios.unc.edu/~wchung/software.html"> here </a>.
<li> Bias correction in genome scans. R code
and an Excel calculator are available
<a href="http://www.bios.unc.edu/~wrightf/genomebias"> here </a>. The paper
can be downloaded <a href="Bias.pdf"> here </a>. 
<li> The software, <a href="../software/sPCA"> 
ShrunkenPCA</a>,
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, <a href="http://genepath.med.harvard.edu/~reich/Software.htm">
EigenSoft </a>.   
<li> Nonparametric Bayesian method for mapping gene-gene interaction. The
manuscript can be downloaded <a
href="http://www.genetics.org/cgi/reprint/186/1/385"> here </a>. So is the
 <a
href="Genegenemap/fbm.new.tar.gz">  software </a>.  You may test the
method by running the sample perl code located in "test" folder. 
<li>Semiparametric multiple QTL mapping method where
the non-genetic covariate effects are modeled 
nonparametrically. <a href="../semiparam/semiparametric.c">
The software </a> and the related <a href="bayesianBiometricsFinal.pdf"> paper
</a> can be downloaded.  Detailed user manual will be posted soon.
<li> The software on Bayesian QTL mapping for RIX data can be downloaded
<a href="BayesianRIX"> here </a>. 
<li> The software on RNA-seq analysis of F1 reciprocal crosses can be downloaded
<a href="rxSeq"> here </a>. 
<li> The software for fast eQTL analysis of twin data can be downloaded
<a href="FasteQTL"> here </a>.