Table 1. Application Programming Interface (API) of Cytoscape commands provided by eXamine.

Figure 1 shows an example workflow using the below commands.

Command	Argument (type)	Description
examine generate groups		Generates eXamine groups from a given set of columns of the node table
	○ network (CyNetwork) ○ selectedGroupColumns (List) ○ useAllNodes (Boolean)	Network for which to generate the groups Columns of the node table from which the groups will be created (comma separated) Indicates whether to use all nodes for group generation, or only those nodes currently selected in Cytoscape
examine select groups		Select groups to be visualized by eXamine
	○ selectedGroup (List)	Group identifiers to select (comma separated)
examine remove groups		Removes all groups generated by eXamine
	○ network (CyNetwork)	Network from which to remove the groups
examine update settings		Updates visualization settings
	○ network (CyNetwork) ○ labelColumn (String) ○ urlColumn (String) ○ scoreColumn (String) ○ showScore (Boolean) ○ selectedGroupColumns (List)	Network to visualize Column of the node table that contains the node labels Column of the node table that contains URLs with additional information about the nodes Column that contains annotation enrichment scores Indicates whether to show annotation enrichment scores Group columns of the node table to show in the visualization
examine interact		Shows the selected network and groups in an interactive visualization window
examine export		Generates an SVG file with a visualization of the selected network and groups
	○ path (String)	Filename