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
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
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.
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
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.
- famtypes A
small utility for sanity-checking and summarizing pedigree files
- whap A
tool for haplotype analysis. whap is a C/C++ program for
haplotype analysis. It can handle SNPs or multiallelic markers;
disease or quantitative traits; unrelated individuals or family-based
samples. In particular, it is possible to test nested models in a
flexible manner that enables various types of conditional analysis
(e.g. whether a particular haplotype can explain all the association
signal at a locus, or whether a particular variant has any effects
independent of the effects of correlated haplotypes). An example
application of whap is described in Curran et al. (2005).
Latent class analysis model for detecting population stratification.
L-POP is a C/C++ program to detect population stratification in
samples of unrelated individuals. It uses an approach similar in
spirit to that used in STRUCTURE, except it is based on latent class
analysis. The method has been described in Purcell & Sham (2004).
Online tool (currently not operational) for genetic association
analysis. This tool provides a simple interface from which
case/control and TDT analyses can be conducted, for the analysis of
one or more samples simultaneously. A number of genetic models can be
compared (e.g. multiplicative, dominant, etc); genotypic relative
risks and/or population allele frequencies can be equated across
samples or tested for heterogeneity.
- LdOOKUP: a webtool for
linakge-disequilibrium aware look-ups into
the PGC and other GWAS
- G x E in twin analysis: Mx scripts for continuous
moderator models This link provides a collection of Mx (a freely
available model-fitting package developed by Mike Neale, that is
commonly used for modeling genetically-informative family data)
scripts that accompany Purcell (2001)
twin analysis: Mx scripts for DF analysis in proband-selected twin
samples. This link provides a collection of Mx scripts that accompany
Purcell & Sham