Software
WGAViewer
WGAViewer is a bioinformatic software tool specifically designed to provide a user-friendly interface to automatically annotate, visualize, and interpret the set of P values emerging from a GWAS study. It can be used to highlight possible functional mechanisms, to help create working hypothesis, and to select genomic regions that may need to be resequenced in a search for candidate causal variants.
MetaP
MetaP performs a meta-analysis and combines the statistical association signals (P values) from independent studies or study populations, taking account of the impacts of sample sizes and effect directions.
SNPExpress
SNPExpress is a database interface that we developed to permit interrogation of the effects of common SNPs on exon and transcript level expression. This database enables researchers to input a SNP, gene, or a genomic region to investigate regions of interest for localized effects of SNPs on exon and gene level expression changes.
GWASpower/QT
GWASpower/QT is a statistical power calculation software designed for genome wide association studies (GWAS) with quantitative traits in natural populations. It allows users to input the effect size as heritability measures, instead of the phenotype means of each genotype of the genetic marker, which is often unavailable in exploratory experiments such as GWAS. Input parameters are heritability (required), type 1 error rate (required), total sample size (required), linkage disequilibrium (optional) and other covariates (optional). The software returns the statistical power and a plot of a family of power curves.