AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

A web application to visualize and edit pathway models

An interactive and collaborative graphical curation tool for cancer pathways

MSigDB gene sets for multiple organisms in a tidy data format

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Scenario analysis notebooks for the IPCC Special Report on Global Warming of 1.5°C

Gene Set Clustering based on Functional annotation

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

A project for exploring differentially active signaling paths related to proteomics datasets

Package to calculate functional similarity between genes https://llrs.github.io/BioCor

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.

A Python package for benchmarking pathway database with functional enrichment and classification methods

Flexible gene set enrichment analysis

Harmonizing pathway databases using Biological Expression Language (BEL)

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

A manually curated database of human gut metabolic modules.

An R package for multi-dimensional pathway enrichment analysis

PathwayMatcher is a free, open-source software to search for pathways related to a list of proteins in Reactome. This repository is the development repository. For the latest version see: https://github.com/PathwayAnalysisPlatform/PathwayMatcher

This repository is in support of the PathCORE-T paper (https://doi.org/10.1101/147645). It contains all the code and necessary data/metadata to repeat all analyses in the paper.

Overrepresentation analysis for KEGG and PID pathways using community detection

Explore biomolecular pathways in Reactome from the command-line or a Python script

python client for reactome content and analysis services api calls

Results of the evaluation of pathway databases using TCGA datasets

Package to analyse gene sets

Disease pathways in the human interactome

A python library for programmatic usage of EBI InterPro Genome Properties.

MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data

A web application for exploring, analyzing, and curating pathway databases

This repository contains the different resources derived or generated using ComPath

Differential gene expression analysis and pathway analysis of RNAseq data