GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. This source code repository represents a version of GEMMA which is under development.
GEMMA as a Service (GEMMA-S - it's a GAAS) is a next generation of the original GEMMA. We decided on a fresh start to create a more service oriented solution. For more information see the big picture.
Check out RELEASE-NOTES.md to see what's new in each GEMMA release.
For the stable release of GEMMA, see the git repository.
For now, GEMMA-S has no real improvements over GEMMA1. For LOCO, parallel compute, permutations and caching, see gemma-wrapper. For validation and BIMBAM/plink/Rqtl2 parsing and conversion see gemma2lib.
To contribute, see the development docs.
Copyright (C) 2012–2021, Xiang Zhou, Pjotr Prins and team.
The GEMMA-S source code repository is free software: you can redistribute it under the terms of the GNU General Public License. All the files in this project are part of GEMMA-S. This project is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. GEMMA and GEMMA-S are published under the GPL-3.0 License. See LICENSE.
For bugs GEMMAv1 has an issue tracker on github. For general support GEMMA has a mailing list at gemma-discussion.
Before posting an issue search the issue tracker and mailing list first. It is likely someone may have encountered something similiar. Also try running the latest version of GEMMA to make sure it has not been fixed already. Support/installation questions should be aimed at the mailing list - it is the best resource to get answers.
The issue tracker is specifically meant for development issues around the software itself. When reporting an issue include the output of the program and the contents of the .log.txt file in the output directory.
By using GEMMA and communicating with its communtity you implicitely agree to abide by the code of conduct as published by the Software Carpentry initiative.
GEMMA-S is developed by
Pjotr Prins
Dept. of Genetics, Genomics and Informatics
University of Tennessee Health Science Center
and
Xiang Zhou
Dept. of Biostatistics
University of Michigan
See also contributors.
The original GEMMA software was developed by:
Xiang Zhou and Pjotr Prins with contributions from Peter Carbonetto, Tim Flutre, Matthew Stephens, and others - see also contributors.