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

G2P
Dataset

G2P Gene2Phenotype

Provides data on genes, variants, phenotypes and disease from the published…

Provides data on genes, variants, phenotypes and disease from the published literature.

RS
Terminology

RS Rat Strain ontology

Permits to annotate rat strains in a standardized manner. RS reflects the…

Permits to annotate rat strains in a standardized manner. RS reflects the breeding history and genetic makeup of the strains to facilitate querying and retrieval, analysis and comparisons amongst…

ORDO
Terminology

ORDO Orphanet Rare Disease Ontology

Provides a terminology for rare diseases derived from the Orphanet database.…

Provides a terminology for rare diseases derived from the Orphanet database. ORDO captures relationships between diseases, genes and other relevant features.

TOP
Terminology

TOP Thesaurus Of Plant characteristics

Offers a terminology for major plant characteristics used in functional…

Offers a terminology for major plant characteristics used in functional ecology. TOP covers about 850 plant characteristics building on existing standards defined in the context of terminological…

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…

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