WGAViewer

Related software tools

This page lists a number of software tools that WGAViewer users may find useful.

(1) PLINK

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. PLINK is being developed by Shaun Purcell at the Center for Human Genetic Research ( CHGR ), Massachusetts General Hospital ( MGH ), and the Broad Institute of Harvard & MIT, with the support of others .

Here is the instruction on how to use the WGAViewer software to load the GWAS results generated from PLINK.

(2) PennCNV

PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays, using a hidden Markov model (HMM). PennCNV is being developed by Kai Wang et al. at the Children's Hospital of Philadelphia.

Here is the instruction on how to use the WGAViewer software to load and annotate the 'rawcnv' file generated from PennCNV.

(3) SNPExpress

SNPExpress is a database that we developed to permit interrogation of the effects of common SNPs on exon and transcript level expression in two different tissue types: brain and PBMC ( Peripheral Blood Mononuclear Cell ). 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.

(4) MetaP

MetaP is a simple online tool to perform 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.