New Cytoscape App: Largest Subnetwork

[Yihang Xin]

We have released a new app in the Cytoscape App Store called Largest Subnetwork. It’s a very simple, yet handy app. It adds a menu item under Select > Nodes to select the Largest Subnetwork in the current network. This operation is useful when working with a partitioned network consisting of two or more distinctly connected graphs. Partition networks are common following MCL clustering, for example, or from importing interactions from databases like STRING (see screenshot).

While this is often better than trying to drag-select a subnetwork by eye, the app is really useful in automation scripts and workflows where you don’t have the option to manually drag-selectl. The basic command syntax is network select subnetwork. You can also optionally specify a network by name or SUID with the network parameter. This will work in RCy3 and py4cytoscape.

Let us know if you have any feedback. Enjoy!

 - Yihang and Alex