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Genotype-phenotype interaction analysis software tools and databases

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…

Genotype-phenotype analysis applications

Most recent bioinformatics tools

fetalfraction-S…
Desktop

fetalfraction-SNPimpute

Surveys fetal fractions using single nucleotide polymorphism (SNP) imputation.…

Surveys fetal fractions using single nucleotide polymorphism (SNP) imputation. fetalfraction-SNPimpute is able to produce accurate results as well as semiconductor sequencing and low coverage to…

MixupMapper
Web

MixupMapper

Detects and corrects sample mix-ups with high sensitivity and specificity.…

Detects and corrects sample mix-ups with high sensitivity and specificity. MixupMapper measures the difference between actual gene expression levels and predicted expression levels that are solely…

fastLSA
Desktop

fastLSA

Allows users to study local similarity analysis (LSA). fastLSA is an algorithm…

Allows users to study local similarity analysis (LSA). fastLSA is an algorithm using a novel asymptotic upper bound algorithm for calculating the LSA p-value. It replaces a computationally intensive…

PRSice
Desktop

PRSice Polygenic Risk Score software

Allows users to capture current standard practices in polygenic risk score…

Allows users to capture current standard practices in polygenic risk score (PRS) studies and the different applications of PRS. PRSice performs a simulation study to estimate a P-value significance…

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…

PheWAS catalog
Dataset

PheWAS catalog

Contains the PheWAS results for 3,144 single-nucleotide polymorphisms (SNPs)…

Contains the PheWAS results for 3,144 single-nucleotide polymorphisms (SNPs) present in the NHGRI GWAS Catalog as of 4/17/2012 in 13,835 European-ancestry individuals from five sites of the…

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…

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