ondina-draia/gene-set-enrichment-analysis-resources

A compilation of packages and web-based apps for Gene Set Enrichement Analysis

Gene Set Enrichement Analysis Resources

Table of Contents

• Web based tools
• R packages
• Python packages
• Other useful apps

About this Repository

In this repository you can find the many resources which are currently freely available for gene set enrichement analysis.

Please note that while this page offers valuable resources, it is not exhaustive and does not list all individual tools.

We welcome contributions! Feel free to open a pull request (PR) to enhance the repository.

Web-based tools

• STRING - STRING is a database of known and predicted protein-protein interactions. It provides a comprehensive resource for the analysis of protein networks and their functional associations.It can also be integrated with Cytoscape, a powerful network visualization tool. This allows for the visualization and analysis of protein-protein interaction networks.
• EnrichR - Enrichr is a web-based tool that allows users to perform gene set enrichment analysis on user-provided gene lists. It integrates with various databases, including Gene Ontology, KEGG, and others. It can also be accessed through R by using the EnrichR package.

R packages

• Cluster profiler - Most used resource with R, does comprehensive functional annotation and gene set enrichment analysis.
• fgsea - Fast Gene Set Enrichment Analysis.
• enrichR - Interface to the Enrichr database for gene set enrichment analysis.
• msigdbr - R package that provides an interface to the Molecular Signatures Database (MSigDB). It allows users to easily access and download gene set collections from MSigDB directly within R.
• DOSE - Disease ontology semantic and enrichment analysis.

Python packages

• GSEApy - Description: Gene Set Enrichment Analysis (GSEA) in Python.
• GOATOOLS - GOATOOLS is a Python library for Gene Ontology (GO) analysis. It provides functionalities for conducting GO term enrichment analysis and visualizing results. GOATOOLS is particularly useful for exploring the functional significance of gene sets in the context of Gene Ontology terms.

Other uselful apps

• Cytoscape - A powerful open-source software platform for visualizing complex networks and integrating them with any type of attribute data. It is widely used for network analysis and visualization, and it can be integrated with various tools and databases, including those for gene set enrichment analysis..
• GSEA software - GSEA is a computational method developed by the Broad Institute for interpreting gene expression data in terms of biological pathways or sets of genes. The GSEA software is used to identify statistically significant enrichment of predefined gene sets in a ranked list of genes.

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Enjoy!