eXamine

A set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.
**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 usage instruction see the [http://homepages.cwi.nl/~elkebir/eXamine/tutorial.pdf 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].

2.0.0

Works with Cytoscape 3.0

Release Notes

Major update to improve: * module layout, * contour visualization, * annotation lists, and * Cytoscape node style integration New feautures: * panning

1.1

Works with Cytoscape 3.0

Release Notes

New features: * scrollable set overview * improved visualization * improved performance

1.0.3

Works with Cytoscape 3.0

Release Notes

Bug fixes: * fixed color map bug * fixed optional group score bug New features: * hovering over an edge highlights the intersection of the sets of the two incident nodes

1.0.2

Works with Cytoscape 3.0

Release Notes

* Optional group score

1.0.1

Works with Cytoscape 3.0

Release Notes

* Improved layout parameters * Enhanced link visualization * Use of default values in control panel

1.0

Works with Cytoscape 3.0

Release Notes

Initial release

CYTOSCAPE 3

Version 2.0.0

License Click here

Released 21 May 2015

Works with Cytoscape 3.0

Download Stats Click here