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Gene set enrichment analysis (GSEA) software tools | Gene expression

A common feature of many current functional genomics technologies, as well as many different types of bioinformatics analyses, is that they output very large lists of genes, typically in the order of hundreds or thousands. Evidently, interpreting…
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DESeq
Desktop

DESeq

A method for differential analysis of RNA-sequencing count data, using…

A method for differential analysis of RNA-sequencing count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a…

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Enrichr
Web
Mobile

Enrichr

An integrative web-based and mobile software application that includes new…

An integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to…

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DAVID
Web

DAVID Database for Annotation, Visualization and Integrated Discovery

A web-based online bioinformatics resource that aims to provide tools for the…

A web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. DAVID has been used by researchers from more than 5000…

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GeneWeaver
Web

GeneWeaver

Combines cross-species data and gene entity integration, scalable hierarchical…

Combines cross-species data and gene entity integration, scalable hierarchical analysis of user data with a community-built and curated data archive of gene sets and gene networks, and tools for data…

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GeneTrail
Web

GeneTrail

A web service allowing the integrated analysis of transcriptomic, miRNomic,…

A web service allowing the integrated analysis of transcriptomic, miRNomic, genomic, and proteomic datasets. GeneTrail offers multiple statistical tests, a large number of predefined reference sets,…

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IMP
Web

IMP Integrative Multi-species Prediction

An interactive web server that enables molecular biologists to interpret…

An interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions…

limma
Desktop

limma Linear Models for Microarray Data

Provides an integrated solution for analysing data from gene expression…

Provides an integrated solution for analysing data from gene expression experiments. limma contains rich features for handling complex experimental designs and for information borrowing to overcome…

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globaltest
Desktop

globaltest

Allows researchers to use prior information on groupings of genes and to…

Allows researchers to use prior information on groupings of genes and to specifically investigate groups of genes that interest them from a biological point of view. When researchers have many…

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piano
Desktop

piano Platform for Integrated Analysis of Omics data

Performs gene set analysis (GSA) using various statistical methods, from…

Performs gene set analysis (GSA) using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The piano package contains functions for combining…

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WebGestalt
Web

WebGestalt WEB-based GEne SeT AnaLysis Toolkit

Permits the management, information retrieval, organization, visualization and…

Permits the management, information retrieval, organization, visualization and statistical analysis of large sets of genes. WebGestalt integrates functional enrichment analysis and information…

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SAFE
Desktop

SAFE Significance Analysis of Function and Expression

Allows to test functional categories in gene expression experiments. SAFE can…

Allows to test functional categories in gene expression experiments. SAFE can be used as a workhorse to investigate possible functional relationships. It can study different standard gene-list…

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RCAS
Web
Desktop

RCAS RNA Centric Annotation System

Provides dynamic genome annotations for custom input files that contain…

Provides dynamic genome annotations for custom input files that contain transcriptomic regions. RCAS enables flexible usage and convenient integration with other bioinformatics workflows. It is not…

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Category
Desktop

Category

Allows to perform category analysis. Category can construct a category…

Allows to perform category analysis. Category can construct a category membership matrix from a list of gene identifiers and their annotated GO categories. Category is a part of GSEA (Gene Set…

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KOBAS
Web

KOBAS KEGG Orthology Based Annotation System

Its purpose is to identify statistically enriched pathways, diseases, and GO…

Its purpose is to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases.

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GSEA
Desktop

GSEA Gene Set Enrichment Analysis

A computational method that determines whether an a priori defined set of genes…

A computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA derives…

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pcot2
Desktop

pcot2

Represents a permutation-based method for investigating changes in the activity…

Represents a permutation-based method for investigating changes in the activity of multigene networks. pcot2 is an effective multivariate statistical procedure which allows to assess the correlation…

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GeneSCF
Desktop

GeneSCF Gene Set Clustering based on Functional annotation

Predicts the functionally relevant biological information for a set of genes in…

Predicts the functionally relevant biological information for a set of genes in a real-time updated manner. GeneSCF is designed to handle information from more than 4000 organisms from freely…

Babelomics
Desktop
Web

Babelomics

A web application for the functional analysis of gene expression and genomic…

A web application for the functional analysis of gene expression and genomic data. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a…

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SeqGSEA
Desktop

SeqGSEA

Provides methods for gene set enrichment analysis of high-throughput RNA-Seq…

Provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data,…

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BicOverlapper
Desktop

BicOverlapper

Allows to visualize complex gene expression analysis results coming from…

Allows to visualize complex gene expression analysis results coming from biclustering algorithms. BicOverlapper visualizes the most relevant aspects of the analysis, including expression data,…

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JEPETTO
Desktop

JEPETTO

Performs integrated gene set analysis using information from interaction,…

Performs integrated gene set analysis using information from interaction, pathways and processes databases. JEPETTO uses the TopoGSA server to identify topological analogies between the user selected…

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GeneMANIA
Web

GeneMANIA

Finds other genes that are related to a set of input genes, using a very large…

Finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression,…

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X2K
Desktop

X2K Expression2Kinases

Identifies upstream regulators likely responsible for observed patterns in…

Identifies upstream regulators likely responsible for observed patterns in genome-wide gene expression. The X2K workflow provides several features: two methods for identifying transcription factors…

T-profiler
Web

T-profiler

Analyzes genome-wide expression patterns in one experiment at a time.…

Analyzes genome-wide expression patterns in one experiment at a time. T-profiler is a web application that uses the t-test to score the difference between the mean expression level of predefined…

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sigPathway
Desktop

sigPathway

Allows to conduct pathway analysis. sigPathway realizes analysis by calculating…

Allows to conduct pathway analysis. sigPathway realizes analysis by calculating different statistics. It generates a list of potential pathways but interpreting that list itself can be…

GenCLiP
Web

GenCLiP

A web-based text-mining server which can analyze human genes with enriched…

A web-based text-mining server which can analyze human genes with enriched keywords and molecular interactions. GenCLiP 2.0 offers two unique features: i) analysis of gene functions with free terms…

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ToppCluster
Web

ToppCluster

A web server application that leverages a powerful enrichment analysis and…

A web server application that leverages a powerful enrichment analysis and underlying data environment for comparative analyses of multiple gene lists. ToppCluster generates heatmaps or connectivity…

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PlantGSEA
Web

PlantGSEA Plant GeneSet Enrichment Analysis toolkit

An online websever for gene set enrichment analysis of plant organisms. The…

An online websever for gene set enrichment analysis of plant organisms. The PlantGSEA was designed to serve researchers from plant community with a user-friendly interface as well as…

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iGA
Desktop

iGA Iterative Group Analysis

Provides an automatic functional annotation of microarray results together with…

Provides an automatic functional annotation of microarray results together with a statistical confidence level for each annotation feature. iGA is based on a comprehensive hypergeometric statistics…

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GATHER
Dataset

GATHER Gene Annotation Tool to Help Explain Relationships

Allows to study the Retinoblastoma/E2 Factor (Rb/E2F) pathway. GATHER permits…

Allows to study the Retinoblastoma/E2 Factor (Rb/E2F) pathway. GATHER permits to find common aspects of biology in these otherwise dissimilar expression profiles showing both the power of expression…

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Lynx
Web

Lynx

A web-based database and a knowledge extraction engine. Lynx supports…

A web-based database and a knowledge extraction engine. Lynx supports annotation and analysis of high-throughput experimental data and generation of weighted hypotheses regarding genes and molecular…

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EDDY
Desktop

EDDY Evaluation of Dependency Differentiality

A statistical test for the differential dependency relationship of a set of…

A statistical test for the differential dependency relationship of a set of genes between two given conditions. For each condition, possible dependency network structures are enumerated and their…

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DEsubs
Desktop

DEsubs

A flexible, computationally fast and efficient tool for exploring…

A flexible, computationally fast and efficient tool for exploring disease-associated gene perturbations contextualized by subpathways in a graph-theoretic framework. DEsubs contains an extensive and…

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ABAEnrichment
Desktop

ABAEnrichment

An R package that tests for expression enrichment in specific brain regions at…

An R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing…

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GSA-Lightning
Desktop

GSA-Lightning

A fast implementation of permutation-based gene set analysis. GSA-Lightning is…

A fast implementation of permutation-based gene set analysis. GSA-Lightning is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is…

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GiANT
Desktop

GiANT

An approach for assessing uncertainty in the definition of gene sets. This is…

An approach for assessing uncertainty in the definition of gene sets. This is an essential step when new gene sets are constructed from domain knowledge or given gene sets are suspected to be…

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AnGeLi
Web

AnGeLi Analysis of Gene Lists

Offers customized methods for gene lists calculation, by systematically…

Offers customized methods for gene lists calculation, by systematically screening a multitude of data sources. AnGeLi is a generic gene list enrichment tool for the analysis of gene lists derived…

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R spider
Web

R spider

Implements the Global Network statistical framework to analyze gene list using…

Implements the Global Network statistical framework to analyze gene list using as reference knowledge a global gene network constructed by combining signaling and metabolic pathways from Reactome and…

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SetRank
Desktop
Web

SetRank

Permits to eliminate many false positive hits in gene set enrichment analysis…

Permits to eliminate many false positive hits in gene set enrichment analysis (GSEA). SetRank discards gene sets that have initially been flagged as significant, if their significance is only due to…

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iNOTE
Desktop

iNOTE Integrative Network Omnibus Total Effect Test

Provides efficient procedures for gene set screening which use self-contained…

Provides efficient procedures for gene set screening which use self-contained hypothesis tests. iNOTE is a robust method to model misspecification. This resource performed with close to optimal power…

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GSAR
Desktop

GSAR Gene Set Analysis in R

Implements self-contained multivariate non-parametric statistical methods…

Implements self-contained multivariate non-parametric statistical methods testing a complex null hypothesis against specific alternatives, such as differences in mean (shift), variance (scale), or…

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PAGE
Desktop

PAGE Parametric Analysis of Gene set Enrichment

Increases the statistical power of the existing gene set enrichment program for…

Increases the statistical power of the existing gene set enrichment program for analysis of subtle changes in microarray data. PAGE is an algorithm that employs fold change between experimental…

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HEAT
Web

HEAT H-InvDB Enrichment Analysis Tool

Identifies automatically features specific to a given human gene set. HEAT is a…

Identifies automatically features specific to a given human gene set. HEAT is a data mining tool that searches H-InvDB annotations that are significantly enriched in a user-defined gene set, as…

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FIDEA
Web

FIDEA

A server for the functional interpretation of differential expression analysis.…

A server for the functional interpretation of differential expression analysis. It is free and open to all users, and there is no login requirement.

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CAsubtype
Desktop

CAsubtype

Identifies gene sets for cancer subtype identification and clinical outcome…

Identifies gene sets for cancer subtype identification and clinical outcome prediction. CAsubtype integrates more than 13,000 annotated gene sets and provides a comprehensive repertoire of candidates…

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MORPHIN
Web

MORPHIN Model Organisms Projected on a Human Integrated Gene Network

A web-based discovery tool for human disease studies. MORPHIN investigates…

A web-based discovery tool for human disease studies. MORPHIN investigates human diseases by an orthology-based projection of a set of model organism genes onto a genome-scale human gene network.…

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PathwAX
Web

PathwAX

A webservice for pathway annotation based on crosstalk derived through FunCoup,…

A webservice for pathway annotation based on crosstalk derived through FunCoup, a framework for genome wide functional association networks. PathwAX runs the BinoX algorithm, which employs…

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NetVenn
Web

NetVenn

A network-based web platform for the comparison and analysis of gene lists by…

A network-based web platform for the comparison and analysis of gene lists by combining Venn diagram and gene set enrichment. The tool can integrate gene sets with differentially expressed gene on…

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AbsFilterGSEA
Desktop

AbsFilterGSEA

Provides an efficient gene-permuting gene-set enrichment analysis (GSEA)…

Provides an efficient gene-permuting gene-set enrichment analysis (GSEA) methods for small replicate RNA-seq data. AbsFilterGSEA provides three modes of gene-permuting GSEA methods: (i) original…

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paraGSEA
Desktop

paraGSEA

Accelerates querying of large-scale transcription profiles all-pairs comparison…

Accelerates querying of large-scale transcription profiles all-pairs comparison and global clustering analysis on transcriptomic datasets. paraGSEA is based on a scalable parallel algorithm. It is…

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NEArender
Desktop

NEArender

Performs network enrichment analysis against functional gene sets, benchmarks…

Performs network enrichment analysis against functional gene sets, benchmarks networks and renders raw gene profile matrices of dimensionality 'Ngenes x Nsamples' into the space of gene set…

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Fuento
Desktop

Fuento

Compares a subset of genes against its background. The functional enrichment…

Compares a subset of genes against its background. The functional enrichment tool (Fuento) outputs only relevant enrichment of gene functions in the set and informs about the probability of picking…

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GeneAnalytics
Web

GeneAnalytics

Allows gene set analysis. GeneAnalytics provides tool for rapid…

Allows gene set analysis. GeneAnalytics provides tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next…

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NeuroMMSig
Web

NeuroMMSig Multimodal Mechanistic Signatures for Neurodegenerative diseases

Provides an interface for users to submit data to the mechanistic subgraphs in…

Provides an interface for users to submit data to the mechanistic subgraphs in the Alzheimer's Disease, Parkinson's Disease and Epilepsy. NeuroMMSig is an online resource for mechanism…

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FUNNEL-GSEA
Desktop
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ASSIGN
Desktop

ASSIGN Adaptive Signature Selection and InteGratioN

A pathway profiling toolkit which enables robust and context-specific pathway…

A pathway profiling toolkit which enables robust and context-specific pathway analyses by efficiently capturing pathway activity in heterogeneous sets of samples and across profiling technologies.…

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stringgaussnet
Desktop

stringgaussnet

Allows inferring gene networks starting from a list of differentially expressed…

Allows inferring gene networks starting from a list of differentially expressed (DE) genes by integrating knowledge-based and co-expression network with ease and flexibility. Stringgaussnet allows…

dslice
Desktop

dslice

Many statistical problems in bioinformatics and genetics can be formulated as…

Many statistical problems in bioinformatics and genetics can be formulated as the testing of associations between a categorical variable and a continuous variable. dslice is an R package to…

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NEAT
Desktop

NEAT Network Enrichment Analysis Test

Aims to overcome some limitations of existing resampling-based tests. The main…

Aims to overcome some limitations of existing resampling-based tests. The main idea behind NEAT is that, under the null hypothesis of no enrichment, the number of links between two gene sets A and B…

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rapidGSEA
Desktop

rapidGSEA rapid Gene Set Enrichment Analysis

Facilitates permutation-based gene set enrichment analysis and for commonly…

Facilitates permutation-based gene set enrichment analysis and for commonly available multi-core CPUs and CUDA-enabled GPUs. rapidGSEA integrates two tools: udaGSEA is a CUDA-accelerated tool using…

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TRAPLINE
Desktop

TRAPLINE Transparent Reproducible and Automated PipeLINE

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides…

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect…

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Gitools
Web

Gitools

A framework for analysis and visualization of multidimensional genomic data…

A framework for analysis and visualization of multidimensional genomic data using interactive heat-maps.

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CopTea
Desktop

CopTea Combinatorial OPTimization based Enrichment Analysis

Gathers many functional enrichment analysis based on combinatorial…

Gathers many functional enrichment analysis based on combinatorial optimization. CopTea also includes a network-based probabilistic generative model which identifies important gene ontology (GO)…

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T2GA
Desktop

T2GA

Performs pathway analysis for quantitative proteomic data of a limited number…

Performs pathway analysis for quantitative proteomic data of a limited number of experiments. T2GA is constructed as a multivariate statistic. It uses the probabilistic confidence score provided by…

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Genes2Networks
Web

Genes2Networks

A web-based software that can help experimental biologists to interpret lists…

A web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of…

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NetProt
Desktop

NetProt

Performs complex-based feature selection with proteomics expression data.…

Performs complex-based feature selection with proteomics expression data. NetProt provides a representative protein complex-based feature selection (PCBFS) methods. It reorders differential proteins…

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FatiScan
Web

FatiScan

Allows studying many relevant functional terms, which include Gene Ontology…

Allows studying many relevant functional terms, which include Gene Ontology (GO). FatiScan can deal with ordered lists of genes independently from the nature of the experiment that originated the…

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QuSAGE
Desktop

QuSAGE Quantitative Set Analysis for Gene Expression

A computational framework for quantitative set analysis of gene expression.…

A computational framework for quantitative set analysis of gene expression. QuSAGE accounts for inter-gene correlations, improves the estimation of the variance inflation factor and, rather than…

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TargetMine
Dataset

TargetMine

An integrated data warehouse based on the versatile InterMine framework, which…

An integrated data warehouse based on the versatile InterMine framework, which models biological entities (such as genes and proteins) as ‘objects’ and their relationships as ‘references’ to…

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miARma-Seq
Desktop

miARma-Seq

Designed for mRNA, miRNA and circRNA identification and differential expression…

Designed for mRNA, miRNA and circRNA identification and differential expression analysis, applicable to any sequenced organism. miARma-Seq is presented as a stand-alone tool that provides different…

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RNAModR
Desktop

RNAModR

Analyses and visualises the transcriptome-wide distribution of mRNA…

Analyses and visualises the transcriptome-wide distribution of mRNA modifications. RNAModR provides functions to map lists of genomic loci of RNA modifications to a reference mRNA transcriptome, and…

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MULSEA
Desktop

MULSEA MUlti-list SElection Algorithm

Seeks to identify combinatorial regulation by multi-factor effectors,…

Seeks to identify combinatorial regulation by multi-factor effectors, consisting of the following components. MULSEA starts with a pivot ranked list and a collection of other ranked lists over the…

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XGSA
Desktop

XGSA

Takes the cross-species homology mapping into consideration when doing gene set…

Takes the cross-species homology mapping into consideration when doing gene set analysis. Simulation experiments confirm that XGSA can avoid false positive discoveries, while maintaining good…

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WormExp
Web

WormExp

A web-based application for a taxon-specific gene set exploration and…

A web-based application for a taxon-specific gene set exploration and enrichment analysis, which is expected to yield novel functional insights into newly determined gene sets. WormExp is based on…

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LRpath
Web
Desktop

LRpath

Performs gene set enrichment testing, an approach used to test for predefined…

Performs gene set enrichment testing, an approach used to test for predefined biologically-relevant gene sets that contain more significant genes from an experimental dataset than expected by chance.…

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Fuzzy-FishNET
Algorithm

Fuzzy-FishNET

Proceed to complex-based feature-selection. Fuzzy-FishNET is able to select…

Proceed to complex-based feature-selection. Fuzzy-FishNET is able to select class-relevant differential complexes and only works when sample classes are real. It is a powerful improvement over its…

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FunCluster
Desktop

FunCluster

Allows to search putatively coregulated biological processes sharing a…

Allows to search putatively coregulated biological processes sharing a significant number of co-expressed genes. FunCluster provides better insights into the regulatory mechanisms controlling the…

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NFPscanner
Web

NFPscanner

Provides a ready-to-use pathway-based network analysis resource with an…

Provides a ready-to-use pathway-based network analysis resource with an interactive user interface. NFPscanner makes use of pathway knowledge and existing algorithms to compare multiple networks in…

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MrGSEA
Desktop

MrGSEA

Offers higher flexibility and functionality in the form of a large scale of…

Offers higher flexibility and functionality in the form of a large scale of ranking metrics, usage of custom gene set database and two different types of permutation. MrGSEA is an implementation of…

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WebGIVI
Web
Desktop

WebGIVI

Permits to visualize and explore gene-informative terms (iTerms) pairs. WebGIVI…

Permits to visualize and explore gene-informative terms (iTerms) pairs. WebGIVI can help biologists in developing hypothesis based on an input gene lists. It generates a high-resolution image based…

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htsint
Desktop

htsint High-Throughput Sequencing INTegrate

A Python package used to create gene sets for the study of high-throughput…

A Python package used to create gene sets for the study of high-throughput sequencing data. The goal is to create functional modules through the integration of heterogeneous types of data. These…

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Q-Gen
Desktop

Q-Gen Generalized QuSAGE

An extension to the gene set analysis method of QuSAGE. Q-Gen allows for linear…

An extension to the gene set analysis method of QuSAGE. Q-Gen allows for linear mixed models to be applied appropriately within a gene set analysis framework. It provides GSA an added layer of…

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npGSEA
Desktop

npGSEA

Agene set enrichment analysis that is computationally inexpensive, and avoids…

Agene set enrichment analysis that is computationally inexpensive, and avoids the resampling granularity issue. npGSEA allows approximate testing to be done orders of magnitude faster than one could…

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ArrayPlex
Desktop

ArrayPlex

A software package that centrally provides a large number of flexible toolsets…

A software package that centrally provides a large number of flexible toolsets useful for functional genomics, including microarray data storage, quality assessments, data visualization, gene…

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YunBe
Desktop

YunBe

A gene set analysis algorithm for biomarker identification in the cloud. YunBe…

A gene set analysis algorithm for biomarker identification in the cloud. YunBe is open-source and freely accessible within the Amazon Elastic MapReduce service.

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ADGO
Web

ADGO

Provides composite interpretations for microarray data comparing two sample…

Provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. Some other tools also incorporate…

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Algal…
Web

Algal Functional Annotation Tool

A bioinformatics resource to functionally interpret gene lists and elucidate…

A bioinformatics resource to functionally interpret gene lists and elucidate underlying biological themes in silico using integrated annotation and expression data.

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SeqGSA
Desktop

SeqGSA

Analyses gene set with length bias adjustment for RNA-seq data. SeqGSA compares…

Analyses gene set with length bias adjustment for RNA-seq data. SeqGSA compares the gene set maxmean statistic against permutations, while also taking into account of the statistics of the other gene…

SANTA
Desktop

SANTA Spatial Analysis of Network Associations

A package which provides methods for measuring the strength of association…

A package which provides methods for measuring the strength of association between a network and a phenotype. SANTA quantifies the strength of association between a gene set and a network, and…

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PathVar
Web

PathVar

Identifies and analyzes deregulation patterns in pathway expression. PathVar…

Identifies and analyzes deregulation patterns in pathway expression. PathVar allows to exploit these patterns to find clusters of similar samples and build sample classification models. The software…

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FungiFun
Web

FungiFun

A user-friendly web tool for functional enrichment analysis of fungal genes and…

A user-friendly web tool for functional enrichment analysis of fungal genes and proteins. FungiFun offers a modern web interface and creates interactive tables, charts and figures, which users can…

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GeneTerm Linker
Web

GeneTerm Linker

Filters and links enriched output data identifying sets of associated genes and…

Filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance.

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ChIP-Enrich
Desktop
Web

ChIP-Enrich

Tests ChIP-seq peak data for enrichment of biological pathways, Gene Ontology…

Tests ChIP-seq peak data for enrichment of biological pathways, Gene Ontology terms, and other types of gene sets. Using an input .BED file, ChIP-Enrich assigns peaks to genes based on a chosen…

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CohenEtAl2017
Desktop

CohenEtAl2017

Allows to detect and assess common signals in multi-electrode…

Allows to detect and assess common signals in multi-electrode neurophysiological recordings. The mathematical analysis framework describes how a common signal influences the estimation of power,…

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JAGST
Desktop

JAGST Just Another Gene-Set Test

Provides gene set tests. JAGST is a suite of three tests: (i) a self-contained…

Provides gene set tests. JAGST is a suite of three tests: (i) a self-contained test that replicates results from a leading self-contained test ROAST, (ii) a power-invariant self-contained test that…

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iDEP
Web
Desktop

iDEP Integrated Differential Expression and Pathway analysis

Analyzes gene expression data from DNA microarray or RNA-Seq. iDEP integrates…

Analyzes gene expression data from DNA microarray or RNA-Seq. iDEP integrates many commonly-used R/Bioconductor packages with comprehensive annotation databases. Normalized expression and RNA-Seq…

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FIGS
Desktop

FIGS Fuzzy Inference of Gene-sets

Identifies multi-functional genes from meta-analysis of context-specific…

Identifies multi-functional genes from meta-analysis of context-specific transcriptomic datasets. FIGS is an application that can be used to obtain gene-sets from matrix defining the pair-wise…

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InfoSigMap
Web

InfoSigMap

Provides a quick navigation into any set of scores associated to the…

Provides a quick navigation into any set of scores associated to the informative signatures. InfoSigMap is a user-friendly interactive Google Maps based tool whose nodes are constituted by our set of…

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MiSTIC
Web
Desktop

MiSTIC Minimum Spanning Trees Inferred Clustering

Visualizes and compares collections of gene expression profiles, instantly…

Visualizes and compares collections of gene expression profiles, instantly highlighting differences and similarities in gene clustering between cancer types or subtypes. MiSTIC should facilitate…

GeoDiver
Web
Desktop

GeoDiver

Analyses Gene Expression Omnibus (GEO) datasets. GeoDiver is a web application…

Analyses Gene Expression Omnibus (GEO) datasets. GeoDiver is a web application which performs Differential Gene Expression Analysis (DGEA) and Generally Applicable Gene-set Enrichment Analysis (GAGE)…

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GSA-Genie
Web

GSA-Genie Gene Set Analysis-Genie

Offers a broad selection of gene sets and statistical methods. GSA-Genie is a…

Offers a broad selection of gene sets and statistical methods. GSA-Genie is a web application and an alternative to other tools and databases. It provides a one-stop, comprehensive solution of…

xCell
Web

xCell

Performs cell type enrichment analysis from gene expression data for 64 immune…

Performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. xCell is a gene signatures-based method learned from thousands of pure cell types from various…

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WTFgenes
Desktop
Web

WTFgenes What’s The Function of these genes?

Interprets experimentally-identified lists of genes. WTFgenes uses…

Interprets experimentally-identified lists of genes. WTFgenes uses hypergeometric and model-based approaches. It permits to know what is the function of different genes thanks to Bayesian Term…

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TopKLists
Desktop

TopKLists

Allows for statistical inference on the lengths of informative (top-k) partial…

Allows for statistical inference on the lengths of informative (top-k) partial lists, for stochastic aggregation of full or partial lists, and for graphical exploration of the input and consolidated…

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Constellation…
Web

Constellation Map

A tool to visualize and interpret the results when enrichment analyses yield a…

A tool to visualize and interpret the results when enrichment analyses yield a long list of significantly enriched gene sets. Constellation Map identifies commonalities that explain the enrichment of…

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GeneSetDB
Web

GeneSetDB

A comprehensive meta-database with associated gene set enrichment analysis…

A comprehensive meta-database with associated gene set enrichment analysis statistical tools, which integrates a large number of other biological databases for gene set analysis.

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mgsa
Desktop

mgsa Model-based gene set analysis

Reduces the number of redundant categories returned by the gene category…

Reduces the number of redundant categories returned by the gene category analysis. mgsa employs probabilistic inference via a Metropolis-Hasting algorithm to estimate the probability of categories to…

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GlobalANCOVA
Desktop

GlobalANCOVA

Summarizes the individual gene-wise linear models to a group statement.…

Summarizes the individual gene-wise linear models to a group statement. GlobalANCOVA is an ANOVA-based sum of squares that offers data and functions as well as a vignette to guide the user through…

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RDAVIDWebServic…
Desktop

RDAVIDWebService

Provides a class-based interface from R programs/scripts to fully…

Provides a class-based interface from R programs/scripts to fully access/control the database for annotation, visualization and integrated discovery, without the need for human interaction on its Web…

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GEO2Enrichr
Web

GEO2Enrichr

A web application and two browser extensions (one for Chrome and another for…

A web application and two browser extensions (one for Chrome and another for Firefox) designed to ease the extraction of signatures from studies posted on the Gene Expression Omnibus (GEO) database.…

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RAMONA
Web

RAMONA

It offers an easy-to-use interface for the simultaneous gene set analysis of…

It offers an easy-to-use interface for the simultaneous gene set analysis of combined omics datasets and is an extension of the previously introduced MONA approach.

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RIDDLE
Web

RIDDLE Reflective Diffusion and Local Extension

Uses well developed guilt-by-association principles upon a human gene network…

Uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. RIDDLE is particularly adept at characterizing sets with no annotations, a major…

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GEPAT
Web

GEPAT Genome Expression Pathway Analysis Tool

A web-based tool offering an integrated analysis of transcriptome data under…

A web-based tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. GEPAT imports various formats of oligonucleotide arrays, cDNA arrays and data…

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AtCAST
Web

AtCAST

A web-based tool to analyze the relationship between experimental conditions…

A web-based tool to analyze the relationship between experimental conditions among transcriptome data. Users can analyze 'user's transcriptome data' of a new mutant or a new chemical…

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BubbleGUM
Desktop

BubbleGUM

A computational tool that allows to automatically extract phenotype signatures…

A computational tool that allows to automatically extract phenotype signatures based on transcriptomic data and to perform easily multiple GSEA runs in a row. The result is displayed at the global…

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ErmineJ
Desktop

ErmineJ

Performs analyses of gene sets in high-throughput genomics data such as gene…

Performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. A typical goal is to determine whether particular biological pathways are "doing…

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WhichGenes
Web

WhichGenes

An on-line, database-free, web-based tool for easily gathering, building,…

An on-line, database-free, web-based tool for easily gathering, building, storing and exporting always updated gene sets coming from multiple data sources. It allows researchers to elaborate custom…

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COFECO
Web

COFECO

A web-based tool for a composite annotation of protein complexes, KEGG pathways…

A web-based tool for a composite annotation of protein complexes, KEGG pathways and Gene Ontology (GO) terms within a class of genes and their orthologs under study. Widely used functional enrichment…

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RuleGO
Web

RuleGO

A web-based application for describing gene groups using logical rules based on…

A web-based application for describing gene groups using logical rules based on Gene Ontology terms. RuleGO takes as an input two lists of genes: a list of genes to be described and a reference list…

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Enrichment Map
Desktop

Enrichment Map

Allows you to visualize the results of gene-set enrichment as a network. It…

Allows you to visualize the results of gene-set enrichment as a network. It will operate on any generic enrichment results as well as specifically on Gene Set Enrichment Analysis (GSEA) results.…

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FGSEA
Desktop

FGSEA Fast Gene Set Enrichment Analysis

Implements a special algorithm to calculate the empirical enrichment score null…

Implements a special algorithm to calculate the empirical enrichment score null distributions simultaneously for all the gene set sizes. FGSEA is a fast gene set enrichment analysis (FGSEA) method…

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GeneAnswers
Desktop

GeneAnswers

Provides an integrated solution for a group of genes and specified categories…

Provides an integrated solution for a group of genes and specified categories (biological or medical functions, such as Gene Ontology, Disease Ontology, KEGG, etc) to reveal the potential…

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Tribe
Web

Tribe

Provides a means for researchers to perform reproducible gene set based…

Provides a means for researchers to perform reproducible gene set based analyses seamlessly across webservers and command line tools. Tribe allows users to create analysis pipelines that use their…

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iPEAP
Desktop

iPEAP integrative Pathway Enrichment Analysis Platform

Handles transcriptomics, proteomics, metabolomics and GWAS data under a unified…

Handles transcriptomics, proteomics, metabolomics and GWAS data under a unified aggregation schema. iPEAP emphasizes on the ability to aggregate various pathway enrichment results generated in…

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NetPathMiner
Desktop

NetPathMiner

A general framework for mining, from genome-scale networks, paths that are…

A general framework for mining, from genome-scale networks, paths that are related to specific experimental conditions.