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Build and share your own Cytoscape workflows with R, Python, and all other standard tools
cyREST is a built-in feature and you don't have to install it separately. However, when the new version of cyREST is available, you can upgrade it anytime from Cytoscape App Store.
Ono, Keiichiro, et al. "CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API." F1000Research 4 (2015).
With cyREST, you can:
- Obtain, create, update, and delete Cytoscape data objects from Jupyter Notebook
- Script your workflows in your favorite programming languages
- cyREST provides programmer-friendly simple RESTful API. This means you can use virtually all kinds of programming languages to access Cytoscape basic functions, such as loading networks, visualizing them with custom Visual Styles, and generating PDF/SVG/PNG files from your network views.
- Wrappers for popular languages - Python and R are two most-widely used programing languages for network data analysis and visualizations. We provides wrappers for those languages for more natural APIs for R and Python programmers.
- RCy3 - Wrapper for R
- py2cytoscape - Wrapper for Python
- Additional info and sample scripts available in the Cytoscape Automation repository
Perfect partner for your existing workflows written in Jupyter Notebooks
- Instead of using limited network visualization features in Python/R libraries, you can use powerful network visualization engine in Cytoscape - without touching your mouse!
- What is cyREST?
- Current version and release history available in the Cytoscape App Store
- Trying Cytoscape Automation
- More examples and tutorials available at the Cytoscape Automation repository
Please send us your feature suggestions and bug reports to our issue tracker, and any questions or concerns to the Cytoscape Help Desk.
- Source Code: The MIT license
- Documentation: CC BY-SA 4.0