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Pathway analysis software tools | Genome-wide association study

Genome-wide association (GWA) studies have typically focused on the analysis of single markers, which often lacks the power to uncover the relatively small effect sizes conferred by most genetic variants. Recently, pathway-based approaches have been…
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…

SigMod
Desktop

SigMod

Integrates genome-wide association studies (GWAS) results and gene network to…

Integrates genome-wide association studies (GWAS) results and gene network to identify a strongly interconnected gene module enriched in high association signals. SigMod is formulated as a binary…

PARIS
Desktop

PARIS Pathway Analysis by Randomization Incorporating Structure

Determines aggregated association signals generated from genome-wide…

Determines aggregated association signals generated from genome-wide association study results. Pathway-based analyses highlight biological pathways associated with phenotypes. PARIS uses a unique…

MAGENTA
Desktop

MAGENTA Meta-Analysis Gene-set Enrichment of variaNT Associations

A computational tool that tests for enrichment of genetic associations in…

A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input. MAGENTA is…

GenGen
Desktop

GenGen

A suite of free software tools to facilitate the analysis of high-throughput…

A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.

SNPsea
Desktop

SNPsea

Identifies the conditions relevant to a trait by assessing the genes within…

Identifies the conditions relevant to a trait by assessing the genes within associated loci for enrichment of condition specificity. SNPsea is a fast, robust and general C++ implementation of a…

traseR
Desktop

traseR TRait-Associated SNP EnRichment analysis

An easy-to-use R Bioconductor package that performs enrichment analyses of…

An easy-to-use R Bioconductor package that performs enrichment analyses of trait-associated SNPs in arbitrary genomic intervals with flexible options, including testing method, type of background and…

aSPU
Desktop

aSPU adaptive Sum of Powered Score Test

We extend two adaptive tests for gene- and pathway-level association with a…

We extend two adaptive tests for gene- and pathway-level association with a univariate trait to the case with GWAS summary statistics without individual-level genotype and phenotype data. We use the…

PAPA
Desktop

PAPA

A flexible tool for pleiotropic pathway analysis utilizing GWAS summary…

A flexible tool for pleiotropic pathway analysis utilizing GWAS summary results. The performance of PAPA was validated using publicly available GWAS summaries of body mass index and waist-hip ratio…

NetDecoder
Desktop
Web

NetDecoder

A network biology-based computational platform designed to integrate…

A network biology-based computational platform designed to integrate transcriptomes, interactomes and gene ontologies to identify phenotype-specific subnetworks. NetDecoder is based on network flow…

MAGMA
Desktop

MAGMA Multi-marker Analysis of GenoMic Annotation

A fast and flexible tool for gene and gene-set analysis of GWAS genotype data.…

A fast and flexible tool for gene and gene-set analysis of GWAS genotype data. The gene analysis is based on a multiple regression model, to provide better statistical performance. The gene-set…

NETAM
Desktop

NETAM NETwork-driven Association Mapping

Detects ‘path associations’ from SNPs to phenotypes through gene expression…

Detects ‘path associations’ from SNPs to phenotypes through gene expression traits. NETAM first constructs an association network, where nodes represent SNPs, gene traits or phenotypes, and edges…

ancGWAS
Desktop

ancGWAS

An algebraic graph-based centrality measure that accounts for linkage…

An algebraic graph-based centrality measure that accounts for linkage disequilibrium in identifying significant disease sub-networks by integrating the association signal from GWAS data sets into the…

EW_dmGWAS
Desktop

EW_dmGWAS

Searches for dense modules in a human protein-protein interaction (PPI)…

Searches for dense modules in a human protein-protein interaction (PPI) network; it has since become a popular tool for network-assisted analysis of genome-wide association studies (GWAS). dmGWAS…

VEGAS2Pathway
Web
Desktop

VEGAS2Pathway

Aggregates association strength of individual markers into pre-specified…

Aggregates association strength of individual markers into pre-specified biological pathways. VEGAS2Pathway is a a versatile pathway-based approach for genome-wide association studies (GWAS) data…

MITHrIL
Algorithm

MITHrIL Mirna enrIched paTHway Impact anaLysis

An algorithm developed for the analysis of signaling pathways. MITHrIL augments…

An algorithm developed for the analysis of signaling pathways. MITHrIL augments pathways with missing regulatory elements, such as microRNAs, and their interactions with genes. The method takes as…

Path
Desktop

Path

Correlates users’ data with biological information from nine bioinformatics…

Correlates users’ data with biological information from nine bioinformatics resources (Seattle SNPs, PharmGKB, IIDB, NCBI, OMIM, Genetic Association Database, dbSNP, KEGG, and UCSC Genome Browser).…

Pascal
Desktop

Pascal Pathway scoring algorithm

An easy-to-use tool for gene scoring and pathway analysis from GWAS results.…

An easy-to-use tool for gene scoring and pathway analysis from GWAS results. Pascal uses external data to estimate linkage disequilibrium. Therefore, the user only needs to supply genome wide SNP…

PUPPI
Desktop

PUPPI Pathway analysis Using Protein-Protein Interaction networks

A pathway association test for genome-wide association studies (GWAS) with…

A pathway association test for genome-wide association studies (GWAS) with case-control samples. PUPPI aggregates the interaction signals in protein-protein interaction (PPI) networks within a…

PINBPA
Desktop

PINBPA Protein Interaction Network-Based Pathway Analysis

A tool to analyze GWAS data in a network fashion. User can easily import GWAS…

A tool to analyze GWAS data in a network fashion. User can easily import GWAS data, draw Manhattan plots, define blocks, prioritize genes with random walk with restart, detect enriched sub-networks…

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…

HNEP
Desktop
Web

HNEP Heterogeneous Network Edge Prediction

Produces biologically-meaningful predictions by integrating multiple…

Produces biologically-meaningful predictions by integrating multiple high-throughput data sources. The approach computes features describing the network topology connecting two nodes. These features…

GSA-SNP
Desktop

GSA-SNP

A gene set analysis software that can process SNP data as well as gene and…

A gene set analysis software that can process SNP data as well as gene and haplotype data. GSA-SNP provides a fast computation and an easy-to-use interface.

Pointer
Desktop

Pointer

Provides a useful framework for the integrative analysis of pharmacogenetic…

Provides a useful framework for the integrative analysis of pharmacogenetic GWAS data, by increasing the power to detect aggregate effects of multiple low risk variants. A key advantage of Pointer is…

PARADIGM-SHIFT
Desktop

PARADIGM-SHIFT

Predicts the impact of a mutation in a tumor sample using algorithm for each…

Predicts the impact of a mutation in a tumor sample using algorithm for each mutated gene. PARADIGM-SHIFT provides a prediction for each gene and each sample in the cohort and thereby brings a…

INRICH
Desktop

INRICH INterval enRICHment analysis

A pathway-based genome-wide association analysis tool that tests for enriched…

A pathway-based genome-wide association analysis tool that tests for enriched association signals of predefined gene-sets across independent genomic intervals. INRICH has wide applicability, fast…

GSEA-SNP
Desktop

GSEA-SNP

Besides improving power for association mapping, it may facilitate the…

Besides improving power for association mapping, it may facilitate the identification of disease-associated SNPs and pathways, as well as the understanding of the underlying biological mechanisms.…

SNP ratio test
Desktop

SNP ratio test

Assesses the enrichment of significant associations from genome-wide…

Assesses the enrichment of significant associations from genome-wide association studies (GWAS) in a pathway context. The SNP ratio test (SRT) compares the proportion of significant to all SNPs…

Postgwas
Desktop

Postgwas

A comprehensive toolkit for post-processing, visualization and advanced…

A comprehensive toolkit for post-processing, visualization and advanced analysis of GWAS results. Postgwas supports virtually all model organisms and represents the first cohesive implementation of…

Pathway-PDT
Desktop

Pathway-PDT

Uses the framework of pedigree disequilibrium test (PDT) for general family…

Uses the framework of pedigree disequilibrium test (PDT) for general family data, to perform pathway analysis based on raw genotypes in family-based GWAS. Pathway-PDT also can be more powerful than…

GWAS module
Desktop

GWAS module

Identifies and integrates tissue-specific functional network with imaging…

Identifies and integrates tissue-specific functional network with imaging genome wide association studies (GWAS) results. GWAS module introduces regression models in addition to classification models…

SIFORM
Desktop

SIFORM Shared Informative FactOR Models

A statistical framework to detect predictive biomarkers for a response variable…

A statistical framework to detect predictive biomarkers for a response variable of interest, which is typically a disease-associated phenotype. SIFORM explores associations between a disease…

NIMMI
Desktop

NIMMI Network Interface Miner for Multigenic Interactions

Helps investigators to prioritize genes and networks related to a particular…

Helps investigators to prioritize genes and networks related to a particular phenotype after a Genome-wide association study (GWAS). NIMMI is an open-source tool that takes into account information…

GRASS
Desktop

GRASS gene set ridge regression in association studies

Summarizes the genetic structure for each gene as eigenSNPs and uses a novel…

Summarizes the genetic structure for each gene as eigenSNPs and uses a novel form of regularized regression technique, termed group ridge regression, to select representative eigenSNPs for each gene…

SNPath
Desktop

SNPath

Contains algorithms for evaluating the association between disease risk and a…

Contains algorithms for evaluating the association between disease risk and a set of SNPs that belongs to the same functional gene set or pathways.

ALIGATOR
Desktop

ALIGATOR Association LIst Go AnnoTatOR

A program for testing for Gene Ontology categories over-represented on a list…

A program for testing for Gene Ontology categories over-represented on a list of significant SNPs from a GWA analysis. This method corrects for linkage disequilibrium between SNPs, variable gene…

snpGeneSets
Desktop

snpGeneSets

A uniform-score gene-set analysis (USGSA) to unify different gene measures by a…

A uniform-score gene-set analysis (USGSA) to unify different gene measures by a uniform score for identifying pathways from GWAS data, and use a pre-generated permutation distribution table to…

GESBAP
Web

GESBAP Gene Set-based Analysis of Polymorphisms

A simple implementation of the GSA strategy for the analysis of genome-wide…

A simple implementation of the GSA strategy for the analysis of genome-wide association studies. GESBAP provides a significant increase in the power testing for this type of studies.

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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