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

GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF

rbioapi: User-Friendly R Interface to Biologic Web Services' API

PathIntegrate Python package for pathway-based multi-omics data integration

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

Integration of pathway-related information from Reactome in BEL

Research into statistical distributions of genomes, proteomes and reactomes

OrientDB graph database version of the Reactome Database

A research biochemical network explorer and genetic cytohistological encyclopedia.

Converts Reactome pathways to GPML format

A compilation of pathway gene sets

Converting SBGN-encoded pathways to the SIF file format

Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last…

Converting SBGN encoded pathways to the SIF file format

some scripts to process transcriptomics and Chip-seq data

A set of GO-CAMs built automatically from Reactome pathways.

pathfinder http://reactome.org/ graph binding

An example on how to use reactome Rest API

Google Summer Of Code 2020.

Curate gene pathway clusters using functional interactions