:: DESCRIPTION
PEPIS is a pipeline that is dedicatedly developed for Polygenic, specifically, Epistatic QTL mapping.
::DEVELOPER
The Zhao Bioinformatics Laboratory
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.
Zhang W, Dai X, Wang Q, Xu S, Zhao PX.
PLoS Comput Biol. 2016 May 25;12(5):e1004925. doi: 10.1371/journal.pcbi.1004925.
:: DESCRIPTION
SSEA (SNP Set Enrichment Analysis) is a new SNP-based pathway analysis software for GWAS studies. SSEA consists of two main steps: selecting representative SNPs for each gene, and performing pathway enrichment analysis using all selected SNPs.
::DEVELOPER
CBCL Lab (Computational Biology and Computational Learning) @ UCI
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lingjie Weng, Fabio Macciardi, Aravind Subramanian, Guia Guffanti, Steven G. Potkin, Zhaoxia Yu, Xiaohui Xie
“SNP-based Pathway Enrichment Analysis for Genome-wide Association Study“;
BMC Bioinformatics 2011, 12:99
:: DESCRIPTION
pyLMM is a fast and lightweight python-based linear mixed-model solver for use in genome-wide association studies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
AlphaBayes is a software package for carrying out genome wide association studies and genomic selection. It implements several Bayesian models and can simultaneously or separately fit SNPs, fixed effects, polygenic, and genetic group effects.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GWAtoolbox is an R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS).
::DEVELOPER
the Center of Biomedicine (CBM) at EURAC research.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Feb 1;28(3):444-5. doi: 10.1093/bioinformatics/btr679.
GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data.
Fuchsberger C, Taliun D, Pramstaller PP, Pattaro C; CKDGen consortium.
:: DESCRIPTION
easyGWAS is designed to be a central resource for the genetics community that frees the user from the tedious tasks of implementing statistical software and managing data and computing resources and that serves the community at large through easy data access, validation and reproduction of GWAS findings.
::DEVELOPER
Machine Learning and Computational Biology Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Dominik Grimm, Bastian Greshake, Stefan Kleeberger, Christoph Lippert, Oliver Stegle, Bernhard Sch?kopf, Detlef Weigel and Karsten Borgwardt:
easyGWAS: An integrated interspecies platform for performing genome-wide association studies,
arXiv preprint arXiv:1212.4788, 2012
:: DESCRIPTION
INRICH is a pathway analysis tool for genome wide association studies, designed for detecting enriched association signals of LD-independent genomic regions within biologically relevant gene sets.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
INRICH: interval-based enrichment analysis for genome-wide association studies.
Lee PH, O’Dushlaine C, Thomas B, Purcell SM.
Bioinformatics. 2012 Jul 1;28(13):1797-9. doi: 10.1093/bioinformatics/bts191.
:: DESCRIPTION
PBOOST is a GPU based tool for parallel permutation tests in genome-wide association studies.
::DEVELOPER
Laboratory for Bioinformatics and Computational Biology, HKUST
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies.
Yang G, Jiang W, Yang Q, Yu W.
Bioinformatics. 2014 Dec 21. pii: btu840.
:: DESCRIPTION
Gowinda is a multi-threaded Java application that allows an unbiased analysis of gene set enrichment for Genome Wide Association Studies.
DEVELOPER
Institute of Population Genetics, University of Veterinary Medicine Vienna
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2012 Aug 1;28(15):2084-5. doi: 10.1093/bioinformatics/bts315. Epub 2012 May 26.
Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.
Kofler R1, Schlötterer C.
