Genome-wide association analysis software tools and databases

Genome-wide association studies (GWASs) have been heralded as a major advance in biomedical discovery, having identified ~2,000 robust associations with complex diseases since 2005.Source text:(Manolio, 2013) Bringing genome-wide association findings into clinical use. Nat Rev…

GWAS analysis steps

Most recent bioinformatics tools

RadialMR
Desktop

RadialMR

Allows user to reproduce radial plots. RadialMR also performs radial regression…

Allows user to reproduce radial plots. RadialMR also performs radial regression for the mendelian randomization (MR)-setting.

SNPinfo
Web

SNPinfo

Provides a toolkit for organize, annotate, and select single nucleotide…

Provides a toolkit for organize, annotate, and select single nucleotide polymorphisms (SNPs). SNPinfo is composed of three pipelines and three additional tools. The platform can be used for either…

DeepWAS
Desktop

DeepWAS

Allows detection of individual regulatory single nucleotide polymorphisms…

Allows detection of individual regulatory single nucleotide polymorphisms (SNPs) from genotypes. DeepWAS proceeds to identification of individual regulatory SNPs by investigating genomic location and…

LDstore
Desktop

LDstore

Enables sharing of linkage disequilibrium (LD) information needed for accurate…

Enables sharing of linkage disequilibrium (LD) information needed for accurate fine-mapping in the era of biobank-scale datasets. LDstore serves for estimation, storage, and seamless sharing of LD…

Most popular analytical software and databases

PLINK
Desktop

PLINK

A free, open-source whole genome association analysis toolset, designed to…

A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on…

SKAT
Desktop

SKAT SNP-set (Sequence) Kernel Association Test

A SNP-set (e.g., a gene or a region) level test for association between a set…

A SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics…

i-GSEA4GWAS
Web

i-GSEA4GWAS improved GSEA for GWAS

A web-based resource for analysis of GWAS data to identify pathways/gene sets…

A web-based resource for analysis of GWAS data to identify pathways/gene sets correlated to certain traits by implementing an improved Gene Set Enrichment Analysis (i-GSEA) approach. i-GSEA4GWAS aims…

PANOGA
Web

PANOGA Pathway and Network Oriented GWAS Analysis

A web server for post-genome-wide associatio analysis. PANOGA supports pathway…

A web server for post-genome-wide associatio analysis. PANOGA supports pathway and network-oriented SNP–phenotype association analysis in a single system without requiring any additional manual…

Curators for GWAS analysis

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