#Cytoscape pathway manual

Supplementary data are available at Bioinformatics online. 32,000 of these sets are available in NDEx, and can be used directly in Cytoscape.

#Cytoscape pathway manual

The latest source code and the plugin can be found at: and, respectively. Through a combination of optical character recognition, machine learning and manual curation, gene sets have been extracted from published pathway figures. The OmniPath App has been developed for Cytoscape 3 in the Java programing language. Thus, it makes possible to directly access the large body of high-quality knowledge provided by OmniPath within Cytoscape for inspection and further use with other tools. We present here the OmniPath App, a Cytoscape plugin to flexibly import data from OmniPath via a simple and intuitive interface. OmniPath combines 61 (and continuously growing) network resources into a comprehensive collection, with over 120 000 interactions. Multiple databases provide valuable information about curated pathways and other resources that can be used to build and analyze networks.