We've developed several freely-available, open-source software packages and webtools for the analysis of genetic — and more recently, sleep — data.

PLINK

A toolset for single nucleotide polymorphism (SNP) and copy number variant (CNV) whole-genome association studies. Includes functions for data management, QC, summary statistics, association analysis and IBD/ancestry inference (Purcell et al., 2007).

PLINK/SEQ

Designed for the analysis of variation data from next-generation sequencing studies (VCF-oriented), primarily exome sequencing studies.

GPC: Genetic Power Calculator

Web service for basic power calculations for case/control and quantitative trait family-based and population-based association studies, and for QTL linkage studies (Purcell et al., 2003 and Sham et al., 2000).

XHMM

Designed to detect copy number variants (CNV) in targetted sequencing studies by an analysis of read depth data (Fromer et al., 2012).

INRICH

Software for gene-set enrichment analysis for GWAS, CNV and other genome-wide study designs, based on a genomic, interval-based permutation scheme (Lee et al., 2012).

psgtools

Software for the analysis of sleep signal data, currently focused on processing EEG signals from EDF files. Still under-development, there is currently no documentation: contact us if you are interested.

LdOOKUP

A webtool for linakge-disequilibrium aware look-ups into the PGC and other GWAS summary results.

Genebook

Genebook is designed to create simple web-based databases that provide results from genetic studies. Think of a genebook as an interactive version of a supplementary table in a typical journal article.

 

Redundant, unsupported software and scripts

These are provided primarily for historical reasons.

Behavior genetics and twin analysis