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

QCEWAS
Desktop

QCEWAS

Enables automated quality control of results files of epigenome-wide…

Enables automated quality control of results files of epigenome-wide association studies (EWAS). QCEWAS produces cohort-specific statistics and graphs to interpret the quality of the results files,…

QRank
Desktop

QRank Quantile Rank-score based test

Provides an easy way to identify eQTLs that are associated with the conditional…

Provides an easy way to identify eQTLs that are associated with the conditional quantile functions of gene expression. QRank is a Quantile Rank-score based test which complements the existing…

EpiMODE
Desktop

EpiMODE epistatic MOdule DEtection

Takes advantage of a Bayesian model with a properly designed Gibbs sampling…

Takes advantage of a Bayesian model with a properly designed Gibbs sampling strategy to facilitate the detection of epistatic modules. It was confirmed via extensive simulation studies that epiMODE…

MAPIT
Desktop

MAPIT MArginal ePIstasis Test

Estimates and tests its marginal epistatic effect, the combined epistatic…

Estimates and tests its marginal epistatic effect, the combined epistatic effect between the examined variant and all other variants. By modeling and inferring the marginal epistatic effects, MAPIT…

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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