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

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

R client for the OmniPath web service

MSigDB gene sets for multiple organisms in a tidy data format

Caleydo - Visualization for Molecular Biology

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

A web application to visualize and edit pathway models

Graph-based modeling environment for biology, including prototype editor and services

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

The ideal tool for exploring global marine biogeochemical cycles.

A web based visualization tool for process description maps in SBGN

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

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

Harmonizing pathway databases using Biological Expression Language (BEL)

PHOsphoproteomic dissecTiOn using Networks

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

R package for WikiPathways API

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

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

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