Optional: Automation - mkutmon/cytoscape-tutorials GitHub Wiki

If you have programming experience, I would suggest you to go through the following tutorial (pay attention to the arrows in the bottom right - some sections have multiple slides and you need to click down instead of right): https://cytoscape.org/cytoscape-tutorials/presentations/advanced-automation-2019-mu.html#/

It will guide you through the basics and give you some examples. Most examples available are currently in R and they provide many example scripts.

There are a few R vignette's that come close to example 1 and 2:

• Layouts and Visualization
• WikiPathways and Cytoscape
• Pathway analysis in R
• Network extension with CyTargetLinker

Feel free to explore the material and ask questions!