:: DESCRIPTION
MULTIPOW calculates the power for both joint and replication-based analysis of general multi-stage genetic association studies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Adv Genet. 2008;60:465-504. doi: 10.1016/S0065-2660(07)00417-8.
Study designs for genome-wide association studies.
Kraft P, Cox DG.
:: DESCRIPTION
RegionalP works by quantifying the degree of over-representation of associated SNPs in a pre-defined genomic region, given a specific definition of statistical significance.
::DEVELOPER
Saw Swee Hock School of Public Health
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Eur J Hum Genet. 2012 Apr;20(4):469-75. doi: 10.1038/ejhg.2011.219. Epub 2011 Nov 30.
A statistical method for region-based meta-analysis of genome-wide association studies in genetically diverse populations.
Wang X, Liu X, Sim X, Xu H, Khor CC, Ong RT, Tay WT, Suo C, Poh WT, Ng DP, Liu J, Aung T, Chia KS, Wong TY, Tai ES, Teo YY.
:: DESCRIPTION
EPISNPmpi is a parallel computing program for epistasis testing in genome-wide association studies for supercomputers and commodity clusters.
epiSNP is a computer package of serial computing programs for genome-wide testing of SNP epistasis and single-locus effects of complex or quantitative traits.
::DEVELOPER
JOHN GARBE AND YANG DA , Department of Animal Science, University of Minnesota
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ma L., H.B. Runesha, D. Dvorkin, J.R. Garbe, and Y. Da. (2008)
Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies.
BMC Bioinformatics 9:315.
:: DESCRIPTION
dmGWAS is designed to identify significant protein-protein interaction (PPI) modules and, from which, the candidate genes for complex diseases by an integrative analysis of GWAS dataset(s) and PPI network.
::DEVELOPER
Bioinformatics and Systems Medicine Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
EW_dmGWAS: Edge-weighted dense module search for genome-wide association studies and gene expression profiles.
Wang Q, Yu H, Zhao Z, Jia P.
Bioinformatics. 2015 Mar 24. pii: btv150.
Jia P, Zheng S, Long J, Zheng W, and Zhao Z (2011)
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.
Bioinformatics 27(1):95-102
:: DESCRIPTION
YAMAS (Yet Another Meta-Analysis Software) is a software for meta-analysis of genome wide association studies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012 Sep 12;13:231. doi: 10.1186/1471-2105-13-231.
Quick, “imputation-free” meta-analysis with proxy-SNPs.
Meesters C1, Leber M, Herold C, Angisch M, Mattheisen M, Drichel D, Lacour A, Becker T.
:: DESCRIPTION
IPGWAS is an integrated pipeline for rational quality control and association analysis of genome-wide genetic studies.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Biochem Biophys Res Commun. 2012 Jun 8;422(3):363-8. doi: 10.1016/j.bbrc.2012.04.117. Epub 2012 Apr 30.
IPGWAS: an integrated pipeline for rational quality control and association analysis of genome-wide genetic studies.
Fan YH1, Song YQ.
:: DESCRIPTION
The R package MultiMeta provides an implementation of the inverse-variance based method for meta-analysis, generalized to an n-dimensional setting.
::DEVELOPER
Dragana Vuckovic <dragana.vuckovic at burlo.trieste.it>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.
Vuckovic D, Gasparini P, Soranzo N, Iotchkova V.
Bioinformatics. 2015 Apr 22. pii: btv222
:: DESCRIPTION
repfdr is a tool for replicability analysis for genome-wide association studies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
repfdr: A tool for replicability analysis for genome-wide association studies.
Heller R, Yaacoby S, Yekutieli D.
Bioinformatics. 2014 Jul 9. pii: btu434.
:: DESCRIPTION
LDetect is a method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Approximately independent linkage disequilibrium blocks in human populations.
Berisa T, Pickrell JK.
Bioinformatics. 2015 Sep 22. pii: btv546
:: DESCRIPTION
FINEMAP is a computationally efficient program for fine-mapping in genomic regions associated with complex diseases and traits via a shotgun stochastic search algorithm (Hans et al., 2007).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FINEMAP: Efficient variable selection using summary data from genome-wide association studies.
Benner C, Spencer CC, Havulinna AS, Salomaa V, Ripatti S, Pirinen M.
Bioinformatics. 2016 Jan 14. pii: btw018.
