Genotype-phenotype interaction analysis software tools and databases

Genotype-phenotype analysis applications

Recent technological advances have expanded the breadth of available omic data, from whole-genome sequencing data, to extensive transcriptomic, methylomic and metabolomic data. A key goal of analyses of these data is the identification of effective models that predict phenotypic…

Genotype-phenotype interaction analysis software tools and databases

Most Recent Tools

PLATO
Desktop
rqt
Desktop

rqt

Offers gene-level genome-wide association study (GWAS) meta-analysis. The rqt…

Offers gene-level genome-wide association study (GWAS) meta-analysis. The rqt package can be easily included into bioinformatics pipeline or used as stand-alone. The workflow of gene-level…

ViSEN
Desktop

ViSEN

Analyzes and visualizes epistatic interactions of both two-way and three-way.…

Analyzes and visualizes epistatic interactions of both two-way and three-way. ViSEN is a network-based analysis and visualization tool for epistasis studies. It not only identifies strong…

GNOVA
Desktop

GNOVA GeNetic cOVariance Analyzer

Estimates annotation-stratified genetic covariance between traits using…

Estimates annotation-stratified genetic covariance between traits using genome-wide association studies (GWAS) summary statistics. GNOVA provides accurate covariance estimates and powerful…

Most Popular Tools

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…

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