:: DESCRIPTION
snpEnrichR is an R package to analyze co-localization of SNPs and their proxies in genomic regions
::DEVELOPER
Computational systems biology group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics, 34 (23), 4112-4114 2018 Dec 1
snpEnrichR: Analyzing Co-Localization of SNPs and Their Proxies in Genomic Regions
Kari Nousiainen , et al.
:: DESCRIPTION
PC-select calculates GWAS association statistics using a data-adaptive GRM that improves power over standard mixed models while simultaneously avoiding confounding from population stratification.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genetics. 2014 Jul;197(3):1045-9. doi: 10.1534/genetics.114.164285. Epub 2014 Apr 29.
Improving the power of GWAS and avoiding confounding from population stratification with PC-Select.
Tucker G, Price AL, Berger B
:: DESCRIPTION
SNPAssociation is a code for testing associations allowing for interactions in genome-wide association studies.
::DEVELOPER
Laboratory for Bioinformatics and Computational Biology, HKUST
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2010 Oct 15;26(20):2517-25. doi: 10.1093/bioinformatics/btq486. Epub 2010 Aug 24.
Detecting two-locus associations allowing for interactions in genome-wide association studies.
Wan X1, Yang C, Yang Q, Xue H, Tang NL, Yu W.
:: DESCRIPTION
PSIKO (Population Structure Inference using Kernel-pca and Optimisation) is a software tool written in C++ for quick and accurate estimation of individual ancestry coefficients of a dataset exhibiting population structure.
::DEVELOPER
The UEA Computational Biology Laboratory at the University of East Anglia (UEA)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS.
Popescu AA, Huber KT.
Bioinformatics. 2015 Jul 2. pii: btv396.
:: DESCRIPTION
B-LORE (Bayesian LOgistic REgression) is a command line tool that creates summary statistics from multiple logistic regression on GWAS data, and combines the summary statistics from multiple studies in a meta-analysis. It can also incorporate functional information about the SNPs from other external sources. Several genetic regions, or loci are preselected for analysis with B-LORE.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
PLoS Genet. 2018 Dec 31;14(12):e1007856. doi: 10.1371/journal.pgen.1007856. eCollection 2018 Dec.
Bayesian multiple logistic regression for case-control GWAS.
Banerjee S, Zeng L, Schunkert H, Söding J.
:: DESCRIPTION
traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.
::DEVELOPER
li chen<li.chen at emory.edu>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.
Chen L, Qin Z.
Bioinformatics. 2015 Dec 18. pii: btv741.
:: DESCRIPTION
SNPfold evaluates the effects of SNPs (Single Nucleotide Polymorphisms) on the ensemble structure of an RNA. It takes as input an RNA sequence and one or more SNPs, and then evaluates the structural consequences of the mutation by computing a WT/SNP correlation coefficient. The smaller the correlation the larger the structural effects of the SNP.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS Genet. 2010 Aug 19;6(8):e1001074. doi: 10.1371/journal.pgen.1001074.
Disease-associated mutations that alter the RNA structural ensemble.
Halvorsen M, Martin JS, Broadaway S, Laederach A.
:: DESCRIPTION
The fGWAS (Function Genome-wide association study) is a new concept to evaluate additive and dominant effect for every SNP and identify the significant SNPs from huge SNP data
::DEVELOPER
Center for Statistical Genetics, Penn State University
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Genet. 2011 Jun;129(6):629-39. doi: 10.1007/s00439-011-0960-6. Epub 2011 Feb 4.
A dynamic model for genome-wide association studies.
Das K, Li J, Wang Z, Tong C, Fu G, Li Y, Xu M, Ahn K, Mauger D, Li R, Wu R.
:: DESCRIPTION
HyperLasso is a software of simultaneous analysis of many SNPs and covariates
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genet Epidemiol. 2010 Dec;34(8):879-91. doi: 10.1002/gepi.20543.
SNP selection in genome-wide and candidate gene studies via penalized logistic regression.
Ayers KL, Cordell HJ.
:: DESCRIPTION
EIGENSOFTplus is a software for enhanced use of Principal Components Analysis for performing GWAS QC and primary analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Weale ME (2010),
“Quality Control for Genome-Wide Association Studies”,
in Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, pp.341-372 (Eds. M. R. Barnes and G. Breen). Humana Press.
