https://github.com/ingoscholtes/pathpy

pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models

analysis data data-mining graph graphical-models machine-learning model-selection multi-order network-analysis networks pathways python sequential-data temporal-correlations temporal-networks

Last synced: 25 Sep 2025

https://github.com/mahmoodlab/survpath

Modeling Dense Multimodal Interactions Between Biological Pathways and Histology for Survival Prediction - CVPR 2024

histology-transcriptomics interpretability mahmoodlab pathology pathology-genomics pathology-representation pathways survpath

Last synced: 05 Apr 2025

https://github.com/saezlab/omnipathr

R client for the OmniPath web service

complexes enzyme-ptm networks networks-biology omnipath pathways proteins

Last synced: 05 Apr 2025

https://github.com/saezlab/OmnipathR

R client for the OmniPath web service

complexes enzyme-ptm networks networks-biology omnipath pathways proteins

Last synced: 18 Jul 2025

https://github.com/igordot/msigdbr

MSigDB gene sets for multiple organisms in a tidy data format

enrichment-analysis gene-sets genomics gsea msigdb pathway-analysis pathways

Last synced: 19 Feb 2026

https://github.com/iVis-at-Bilkent/sbgnviz.js

A web based visualization tool for process description maps in SBGN

bioinformatics network-visualization pathways sbgn systems-biology

Last synced: 09 Jul 2025

https://github.com/caleydo/pathfinder

Pathfinder is a tool for the visual exploration of paths in large graphs.

pathfinder pathways phovea phovea-application

Last synced: 19 Jan 2026

https://github.com/jdrudolph/photon

PHOsphoproteomic dissecTiOn using Networks

bioinformatics biological-data-analysis biology pathways phosphoproteomics phosphorylation proteomics signaling-networks signaling-pathways

Last synced: 11 Feb 2026

https://github.com/llrs/biocor

Package to calculate functional similarity between genes https://biocor.llrs.dev

bioconductor-packages bioinformatics functional-similarity gene gene-sets pathway-analysis pathways similarity similarity-measurement

Last synced: 21 Sep 2025

https://github.com/bio2bel/kegg

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

biological-expression-language kegg networks-biology pathways proteins systems-biology

Last synced: 14 Dec 2025

https://github.com/iVis-at-Bilkent/syblars

SyBLaRS: Systems Biology Layout & Rendering Service

bioinformatics graph-algorithms graph-drawing graphviz network-visualization pathway-analysis pathways systems-biology

Last synced: 09 May 2025

https://github.com/geneontology/noctua-models

This is the data repository for the models created and edited with the Noctua tool stack for GO.

annotation geneontology go-cam noctua-models ontology pathways

Last synced: 15 Jan 2026

https://github.com/greenelab/tad_pathways_pipeline

Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

analysis candidate-genes gwas methodology pathways tad tads workflow

Last synced: 05 May 2025

https://github.com/awell-health/developer-hub

Awell's Developer Hub website.

graphql healthcare orchestration pathways workflows

Last synced: 08 Jul 2025

https://github.com/sales-lab/graphite

GRAPH Interaction from pathway Topological Environment

bioinformatics mirror pathway-analysis pathways r

Last synced: 09 Jan 2026

https://github.com/rosscm/fedup

Bioconductor package for pathway enrichment and depletion analysis via a Fisher's exact test on custom test sets and annotations

bioconductor enrichment network pathways

Last synced: 07 Sep 2025

https://github.com/bio2bel/reactome

Integration of pathway-related information from Reactome in BEL

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

Last synced: 29 Jan 2026

https://github.com/derhuerst/extract-gtfs-pathways

Command-line tool to extract pathways from a GTFS dataset.

accessibility cli geojson gtfs pathways public-transport transit

Last synced: 15 Apr 2025

https://github.com/hemekg/hemekg

Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders

biological-expression-language heme knowledge-modeling networks-biology pathways pybel systems-biology

Last synced: 14 Jan 2026

https://github.com/bio2bel/wikipathways

Integration of pathway-related information from WikiPathways in BEL

biological-expression-language pathways systems-biology wikipathways

Last synced: 29 Jan 2026

https://github.com/dhimmel/pathways

A compilation of pathway gene sets

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

Last synced: 23 Mar 2025

https://github.com/emiliesecherre/famat

Functional analysis of metabolic and transcriptomic data

compound gene-ontology genes pathways shiny

Last synced: 18 Feb 2026

https://github.com/pathwayforte/reproducibility-survey

Evaluating the reprodubility of top-ranked publications

enrichment-analysis pathways reproducible-research

Last synced: 05 Mar 2025

https://github.com/bio2bel/go

A Bio2BEL package for converting the Gene Ontology (GO) to BEL

biological-expression-language gene-ontology networks-biology ontology pathways systems-biology terminology

Last synced: 29 Jan 2026

https://github.com/frederikprijck/angular-escher

An Angular application integrating escher for visualizing biological pathways.

angular escher pathways rxjs typescript

Last synced: 06 May 2026

https://github.com/greenelab/netscape

Exploring the network/pathway regularization landscape for gene expression data

analysis gene-expression methodology networks pathways tool

Last synced: 09 May 2026

https://github.com/ruchabhattjoshi/composepathways

this is a sample app following jetpack pathways.

jetpackcompose kotlin pathways

Last synced: 31 Dec 2025

https://github.com/larsgw/gpml-rhea

Collect chemical reactions from a GPML file and look for matching Rhea equations.

biology chemistry gpml pathways wikipathways wikipathways-gpml-files

Last synced: 24 Feb 2025

https://github.com/marinoandrea/stargate-x

Python implementation of a bipartite directed multigraph extracted from the Reactome biological pathway database.

biology bipartite graph pathway pathways reactome reactome-database reactome-graph

Last synced: 17 Mar 2025

https://github.com/andrawaag/pathway_interaction_models

interactions pathways

Last synced: 16 Mar 2025

https://github.com/kkmann/pwcuratr

Curate gene pathway clusters using functional interactions

curation pathways reactome

Last synced: 03 Apr 2025