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 .