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

SDOP-DB
Dataset

SDOP-DB Standardized Description of Operating Procedures DataBase

Enables users to directly compare detailed protocol differences among…

Enables users to directly compare detailed protocol differences among institutes and laboratories. SDOP-DB is a comparative standardized-protocol and a practical application to share, compare and…

SNPxGE2
Dataset

SNPxGE2

Provides results of a comprehensive analysis of single nucleotide polymorphism…

Provides results of a comprehensive analysis of single nucleotide polymorphism (SNP)–coexpression associations in human. SNPxGE2 uses associations based on practical three-way association models…

VarySysDB
Dataset

VarySysDB

Offers information encompassing published genetic polymorphisms. VarySysDB is a…

Offers information encompassing published genetic polymorphisms. VarySysDB is a database that provides separately annotated genetic polymorphisms for each H-inv transcripts (HITs), even from multiple…

G2Cdb
Dataset

G2Cdb Genes to Cognition database

Collects information about the role of synapse proteins in physiology and…

Collects information about the role of synapse proteins in physiology and disease. G2Cdb intends to centralize warehousing data on the synaptic proteome. The database includes mouse and human genomic…

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…

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