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reactome

Here are 31 public repositories matching this topic...

dvklopfenstein / ReactomePy

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

bioinformatics bioinformatics-pipeline pathway-analysis reactome molecular-biology bioinformatics-analysis protein-protein-interaction bioinformatics-scripts biotechnology biological-networks biotech pathway-models bioinformatics-tool reactome-pathway pathway-enrichment-analysis

Updated Oct 12, 2024
Python

moosa-r / rbioapi

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

cran bioinformatics enrichment r string biology api-client rstats uniprot reactome enrichment-analysis jaspar panther enrichr over-representation-analysis rstats-package mieaa

Updated Jan 26, 2026
R

decodebiology / geneSCF_inactive

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

gene-annotation gene-ontology pathways kegg pathway-analysis reactome kegg-pathway real-time-analytics enrichment-analysis real-time-processing functional-analysis kegg-gene gene-set-clustering

Updated Oct 30, 2020
Perl

cwieder / PathIntegrate

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

sklearn metabolomics pathway-analysis reactome multi-omics-integration

Updated Nov 9, 2024
Jupyter Notebook

PathwayAnalysisPlatform / PathwayMatcher_Dev

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

development pathways pathway-analysis reactome biological-networks proteoforms

Updated Mar 4, 2019
Java

linas / biome-distribution

Research into statistical distributions of genomes, proteomes and reactomes

proteomics reactome genomic-data-analysis genomics-visualization proteogenomics reactome-pathway

Updated Feb 14, 2022
Scheme

bio2bel / reactome

Integration of pathway-related information from Reactome in BEL

pathways reactome biological-expression-language networks-biology system-biology

Updated Nov 18, 2020
Python

santo-it / reactome-orientdb

OrientDB graph database version of the Reactome Database

orientdb reactome

Updated Jul 8, 2017

dhimmel / pathways

A compilation of pathway gene sets

tsv human rephetio hetionet genes pathways wikipathways reactome pathway-interaction-database pathway-commons

Updated Apr 2, 2016
Jupyter Notebook

cannin / sbgn2sif

Converting SBGN-encoded pathways to the SIF file format

pathways kegg reactome sbgn biological-networks sif sbgnml sbgn2sif sbgn-to-sif

Updated May 8, 2020
Python

francescopatane96 / RNA-seq_Pipeline

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…

Updated Apr 14, 2023
Jupyter Notebook

MuhammadMuneeb007 / PhenotypeToGeneDownloaderR

A comprehensive bioinformatics pipeline for downloading and analyzing genes associated with specific phenotypes from multiple biological databases. This package provides both R scripts for gene retrieval and Python analysis tools for downstream analysis.

bioinformatics r genomics computational-biology gtex phenotypes uniprot opentargets kegg reactome disgenet disease-gene-association hpo omim gene-prioritization literature-mining string-db phenotype-to-gene

Updated Apr 28, 2026
Python

RichardMatzko / BioNexusSentinel

A research biochemical network explorer and genetic cytohistological encyclopedia.

rna-seq genetics synthetic-biology systems-biology gene-expression reactome reaction-networks

Updated Apr 4, 2024
Python

arnaudporet / sbgn2sif

Converting SBGN encoded pathways to the SIF file format

converter signaling-pathways pathways reactome sbgn biological-networks sif sbgnml sbgn-ml sif-file-format reactome-pathways sbgn-file-format sbgn2sif sbgn-to-sif

Updated Apr 22, 2020
Python

wikipathways / reactome2gpml-converter

Converts Reactome pathways to GPML format

wikipathways reactome pathway gpml

Updated Mar 30, 2023
Java

aprezvykh / bioinformatics

some scripts to process transcriptomics and Chip-seq data

r rnaseq deseq2 reactome edger gage gsea pathview topgo

Updated May 10, 2019
R

geneontology / reactome-go-cams

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

pathways reactome geneontology reactome-pathway noctua-models go-cam

Updated Apr 10, 2026

julianbbenson / GSoC_2026_MP_BioPath

A polyglot (Python/R/Julia) integration pipeline to transition the MP-BioPath Reactome algorithm into a high-throughput genomic predictive engine.

bioinformatics julia systems-biology reactome gsoc-2026

Updated Mar 24, 2026
Python

riyavsinha / reactome-anywidget

An AnyWidget component for interactive embedding of Reactome Pathway browsers

bioinformatics reactome anywidget

Updated Feb 19, 2025
Python

nursa-reactome / gsea-desktop

This fork is intended solely for generating a GSEA jar file that is compatible with Reactome.

reactome

Updated Jul 11, 2019
Java

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