sleep epidemiology, genetics & neurophysiology

Brigham & Women's Hospital, Harvard Medical School, Boston

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


Software for the analysis of sleep signal data, currently focused on processing EEG signals from EDF files. Includes an R library (lunaR) and is also available as a Docker image.

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).
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).


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


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).

Designed for the analysis of variation data from next-generation sequencing studies (VCF-oriented), primarily exome sequencing studies.
An introductory online tutorial to twin analysis, this site provides a collection of modules I created in 2001, designed to offer a gentle introduction to some of the fundamental quantitative genetic concepts in twin studies. In addition, some simple descriptions of other statistical genetic concepts such as linkage disequilibrium and maximum likelihood estimation can be found by following this the above link.

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.