Hello, Is the cytohubba module of Cytoscape available in RCy3 (https://www.bioconductor.org/packages/release/bioc/html/RCy3.html). I did not fine the relevant vignette.

In general, Cytoscape apps are not covered directly by RCy3 methods and thus are not in our vignettes. However, we provide generic access to run any commands that the app authors have exposed through the commandsRun() method in RCy3.

So, to determine whether a particular app supports commands and thus can be run via RCy3, you should check its app page at the Cytoscape App Store: https://apps.cytoscape.org/apps/cytohubba.

This page would have an automation icon and structured link (right side panels) if the authors did support automation, but unfortunately it looks like their last update was in 2017 and they do not.

Another way to check is to browse the Swagger docs for commands (with the app installed) and you should find a namespace like "cytohubba" with their commands. Swagger docs are accessible from Help > Automation in Cytoscape or commandsAPI() in R. Unfortunately, I don't see any commands for CytoHubba.

You can contact the app authors (email info on App Store page) and even submit code to their open source project if you want to pursue adding automation support to their app.