CyTargetLinker graphical user interface
You can use the app from within the Cytoscape user interface.
The best way to learn how the app works, is by going through one of the tutorials available here.
CyTargetLinker application programming interface (API)
Since version 4.0.0, you now also access CyTargetLinker functionality through its API from the Cytoscape command tool or other programming languages like R and Phyton.
A general description of the API can be found here.
For tutorials on how to run CyTargetLinker from R check here.