GxEscanR 2.0.2 – Detect GxE interactions in a Genome-wide Association Study

GxEscanR 2.0.2

:: DESCRIPTION

GxEscan detects GxE Interactions in a Genome-wide Association Study

::DEVELOPER

USC Biostats

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GxEscan

:: MORE INFORMATION

Citation:

Genet Epidemiol. 2013 Sep;37(6):603-13. doi: 10.1002/gepi.21748. Epub 2013 Jul 19.
Finding novel genes by testing G × E interactions in a genome-wide association study.
Gauderman WJ1, Zhang P, Morrison JL, Lewinger JP.

QCGWAS 1.0-8 – Quality Control of Genome Wide Association Study results

QCGWAS 1.0-8

:: DESCRIPTION

QCGWAS is an R package that automates the quality control of genome-wide association result files.

::DEVELOPER

Peter J. van der Most <p.j.van.der.most at umcg.nl> and Ilja M. Nolte

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • R

:: DOWNLOAD

 QCGWAS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 13.
QCGWAS: A flexible R package for automated quality control of genome-wide association results.
van der Most PJ1, Vaez A, Prins BP, Munoz ML, Snieder H, Alizadeh BZ, Nolte IM.

PAPA 1.0 – Identifying Pleiotropic Pathways using Genome-wide Association Study Summaries

PAPA 1.0

:: DESCRIPTION

PAPA is a flexible tool for pleiotropic pathway analysis utilizing GWAS summary results.

:: DEVELOPER

PAPA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R

:: DOWNLOAD

 PAPA

:: MORE INFORMATION

Citation

PAPA: a flexible tool for identifying pleiotropic pathways using genome-wide association study summaries.
Wen Y, Wang W, Guo X, Zhang F.
Bioinformatics. 2015 Nov 14. pii: btv668.

geneSLOPE 0.37.0 – Genome-Wide Association Study with SLOPE

geneSLOPE 0.37.0

:: DESCRIPTION

geneSLOPE is a method for estimating the vector of coefficients in linear model. In the first step of GWAS, SNPs are clumped according to their correlations and distances. Then, SLOPE is performed on data where each clump has one representative.

::DEVELOPER

geneSLOPE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • R package

:: DOWNLOAD

geneSLOPE

:: MORE INFORMATION

Citation

Brzyski D, Peterson CB, Sobczyk P, Candès EJ, Bogdan M, Sabatti C.
Controlling the Rate of GWAS False Discoveries.
Genetics. 2017 Jan;205(1):61-75. doi: 10.1534/genetics.116.193987. Epub 2016 Oct 26. PMID: 27784720; PMCID: PMC5223524.

GWAS4D – Multidimensional Analysis of Context-specific Regulatory Variant for Human Complex Diseases and Traits

GWAS4D

:: DESCRIPTION

GWAS4D is designed to systematically analyze GWAS summary data and identify context-specific regulatory variants by integrating latest multidimensional functional genomics resources and our recently published algorithms. In general, the web server introduces following six major features: (1) prioritizes the regulatory variant by cepip (Li MJ et.al. Genome Biology. 2017); (2) incorporates 127 tissue/cell type-specific epigenomes data; (3) integrates and refines TF motifs from eight public resources for 1480 transcriptional regulators; (4) uniformly processes Hi-C data and calls significant interactions at 5kb resolution across 45 tissues/cell types, links variant to its target regions; (5) annotates non-coding variant with comprehensive functional annotations; (6) equips a highly interactive visualization function for variant-target interaction.

::DEVELOPER

GWAS4D team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Huang D, Yi X, Zhang S, Zheng Z, Wang P, Xuan C, Sham PC, Wang J, Li MJ*.
GWAS4D: Multidimensional analysis of context-specific regulatory variant for human complex diseases and traits.
Nucleic Acids Res. 2018; gky407

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W150-8. doi: 10.1093/nar/gkt456.
GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications.
Li MJ, Wang LY, Xia Z, Sham PC, Wang J.

Matapax – Genome Wide Association Study Web Platform

Matapax

:: DESCRIPTION

Matapax is a platform for high throughput collaborative genome wide association studies (GWAS). Computational time is reduced by processing user-supplied trait data in parallel. Result analysis is facilitated by displaying annotated candidate markers in tabular format and in a genome browser.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Plant Physiol. 2012 Apr;158(4):1534-41. Epub 2012 Feb 21.
Matapax: an online high-throughput genome-wide association study pipeline.
Childs LH, Lisec J, Walther D.

ICSNPathway 1.1 – Identify Candidate Causal SNPs and Pathways from Genome-wide Association Study

ICSNPathway 1.1

:: DESCRIPTION

ICSNPathway is a web server developed to discover candidate causal SNPs and corresponding candidate causal pathways from genome-wide association study (GWAS).

::DEVELOPER

Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

  ICSNPathway

:: MORE INFORMATION

Citation

K. Zhang, S. Chang, et al. (2011).
ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.”
Nucleic Acids Res. 39(suppl 2): W437-W443.

i-GSEA4GWAS 1.1 – Improved-Gene Set Enrichment Analysis for Genome-Wide Association Study

i-GSEA4GWAS 1.1

:: DESCRIPTION

The i-GSEA4GWAS (improved GSEA for GWAS) web server is a web-based resource for analysis of GWAS data (typically each SNP’s -log(P-value)) to identify pathways/gene sets correlated to certain traits by implementing an improved Gene Set Enrichment Analysis (i-GSEA) approach. i-GSEA4GWAS aims to establish an open platform to help further interpret the GWAS data to provide new insights in complex disease study, especially in complementation to the standard single variant/gene based analysis.

::DEVELOPER

Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

   i-GSEA4GWAS

:: MORE INFORMATION

Citation

i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study.
Kunlin Zhang; Sijia Cui; Suhua Chang; Liuyan Zhang; Jing Wang
Nucleic Acids Research 2010; doi: 10.1093/nar/gkq324

TEAM 0.0.4 – Two-locus Epistasis tests in human Genome-wide Association Study

TEAM 0.0.4

:: DESCRIPTION

TEAM is a software significantly speeds up epistasis detection for human GWAS.

::DEVELOPER

the UNC Computational Genetics Working Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 TEAM

:: MORE INFORMATION

Citation

Xiang Zhang, Shunping Huang, Fei Zou and Wei Wang
TEAM: Efficient Two-Locus Epistasis Tests in Human Genome-Wide Association Study
Bioinformatics (2010) 26 (12): i217-i227.