**eXamine** is a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. eXamine extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours.
Click [http://youtu.be/LFGKek_pgjw here] to see eXamine in action,
and click [https://github.com/ls-cwi/examine/blob/master/data/examine_use_case.cys?raw=true here] for the corresponding ready-to-use Cytoscape session file.
For instructions, please see the [https://raw.githubusercontent.com/ls-cwi/eXamine/master/doc/tutorial/tutorial.pdf GUI totorial]
and the [https://github.com/ls-cwi/eXamine/blob/master/doc/tutorial/eXamineNotebook/eXamineTutorial.ipynb commands tutorial].
The code repository is accessible on [https://github.com/ls-cwi/examine github].
If you find eXamine useful, please cite:
Dinkla et al.: eXamine: Exploring annotated modules in networks. [http://www.biomedcentral.com/1471-2105/15/201# BMC Bioinformatics 2014 15:201].
