The following software packages can be downloaded freely. If you find them useful, please email Comments and suggestions are welcome! If you are using Mac OS, please read this.
GENOME A rapid coalescent-based whole genome simulator
mRNA by SNP Browser The database contains association results of 50k transcripts with 400K SNPs.
The R package to calculate the optimal number of repeated measures for quantitative trait linkage analysis.
GSM Genotype-based matching to correct for population stratification in large-scale case-control Genetic Association Studies.
The MQLS program for case-control association testing with related individals using genotype or allele dosage data
Web-based browser for gene expression analysis using imputed HapMap genotypes
eQTL weighted GWAS R function to perform genome-wide association analysis guided by eQTL information
Cross tissue methylation R package to learn methylation relationship between tissues
MetProc  R package for metabolomic data processing
IDCheck R package for detection of sample contamination in RNA-seq data