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

Exhaustive-IGain
Algorithm

Exhaustive-IGain Exhaustive Information Gain

Discovers interactions from a real clinical breast cancer dataset.…

Discovers interactions from a real clinical breast cancer dataset. Exhaustive-IGain uses information gain and Bayesian Network (BN) scoring to learn interactions. It was used to learn interactions…

MBS-IGain
Algorithm

MBS-IGain Multiple Beam Search with Information Gain

Identifies interactive effects in high-dimensional datasets. MBS-IGain employs…

Identifies interactive effects in high-dimensional datasets. MBS-IGain employs information gain to determine whether to add a predictor on a given beam rather than using the score. It uses the score…

BNPP
Algorithm

BNPP Bayesian Network Posterior Probability

Handles multi-locus hypotheses by computing the posterior probability of a…

Handles multi-locus hypotheses by computing the posterior probability of a hypothesis. BNPP allows users to compute the posterior probability of multi-locus models. It represents models where a…

MBS
Algorithm

MBS Multiple Beam Search

Discovers genome-phenome relationship using Bayesian Networks (BNs). MBS…

Discovers genome-phenome relationship using Bayesian Networks (BNs). MBS employs the extended greedy search and learn directed acyclic graph (DAG) models that contain two or more predictors in the…

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…

CADD
Desktop

CADD Combined Annotation Dependent Depletion

Scores the deleteriousness of single nucleotide variants as well as…

Scores the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. CADD integrates many diverse annotations into a quantitative score. The basis of…

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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