eXamine is a Cytoscape app for a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.
Apache Maven is required to compile the code via:
We recommend to install eXamine from the Cytoscape app store.
eXamine can be used in two different ways. First, eXamine can be operated through the Cytoscape GUI (described here). Second, eXamine can be operated through the Cytoscape command interface from either Python (described here and here) or R (described here and here). For both cases the typical workflow is depicted below.