GenABEL: an R library for Genome-wide association analysis

GenABEL

Achievements & publicity

A New-York Times article about R, also mentioning GenABEL (New York Times)
Novel Multiple Sclerosis locus and pathway identified using GenABEL (Nature Genetics)
Six novel lipid level loci identified with the help of *ABEL products (Nature Genetics)
Novel height locus identified with the help of *ABEL products (Human Molecular Genetics)
Eye colour loci discovered using GenABEL (American Journal of Human Genetics)
so on ...

GenABEL is a software created to facilitate whole-genome association analysis. Specific features of GenABEL include

Optimal memory managment
Support of modern methods for analysis in outbred populations
Analysis of survival data
Maximum Likelihood estimation of linear, logistic and Cox regression on genome-wide scale
A range of functions specifically designed to help GWA analysis in samples of individuals from genetically isolated populations, and/or samples of related individuals (family-based design), and other analysis in presence of stratification
Special functions oriented to meta-analysis
Extensive documentation (about 100 pages of reference manual and 150 pages of tutorial)
Many example data sets and exercises

At this page, you can find

GenABEL package
Documentation
Links to related GWA software (ProbABEL -- analysis of imputed data, MetABEL -- meta-analysis)

Last version is 1.4-5 (updated on September 16, 2009)
GenABEL_1.4-5.tar.gz	GenABEL source code (Linux distribution)
GenABEL_1.4-4_R_i386-apple-darwin9.6.0.tar.gz	GenABEL binary for Mac OS, produced on Mac OS X 10.5.5
GenABEL_1.4-4.zip	GenABEL binary for Windows
CHANGES.LOG	The log-file of changes since last version
Old versions	Older versions of GenABEL can be found here

Documentation
ABEL-tutorial.pdf	Using GenABEL, MetABEL and ProbABEL for whole genome association studies. Most of the data used in exercises are part of the GenABEL distribution. Slides on theoretical background, and additional data sets used in exercises, are available from Yurii Aulchenko's page. Look up "Course Material" for ge03-2008 (ge03data.zip, RData supplements for introductory chapters and analysis with stratification) and ge05-2008 (RData supplements for analysis in genetically isolated populations and family data).
GenABEL-manual.pdf	Manual in PDF format

To run under Windows, first install R statistical computing software. Download and save GenABEL_1.4-4.zip. Start R, choose "Packages", then "Install package(s) from local zip files..." and select the GenABEL_1.4-4.zip. Start with command "library(GenABEL)". To see what it can do, try "demo(srdta)". Under Windows, if you do not have Administrator's priviliges, this may well not work. In this case, try out demo(srdtawin).

Contact & Registration

We will appreciate your comments and sugestions about GenABEL. Please do not hesitate to contact Yurii Aulchenko. Please send an e-mail to Yurii if you would like to register for the GenABEL mailing list.

GenABEL: an R library for Genome-wide association analysis

GenABEL

Last version is 1.4-5 (updated on September 16, 2009)

Documentation

Contact & Registration

Related material and links