GeneMANIA

Imports interaction networks from public databases from a list of genes with their annotations and putative functions.
The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses a large database of functional interaction networks from multiple organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data. The plugin follows the look and feel of the GeneMANIA website, but provides more features for power-users: - Number of query genes is limited only by the amount of memory available - Powerful command line tools to automate basic and advanced analysis not available via the website - Users can add their own organisms - Integration with the popular Cytoscape network visualization and analysis platform so Cytoscape networks can be imported into GeneMANIA and GeneMANIA results can be used in other Cytoscape analysis. Also, results can be saved in Cytoscape session files for later work, backup or sharing with colleagues.

3.4.1

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

* Fixes a bug that could freeze Cytoscape when opening session files.

3.4.0

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

* Added a GeneMANIA version of "Prefuse Force Directed Layout" which can ignore hidden nodes/edges and is optimized for GeneMANIA. This layout is now applied by default to GeneMANIA-generated network views. * Improved the error message which is displayed when there is a network issue that prevents the app from connecting to the GeneMANIA server or from downloading a data set. * Disabling GeneMANIA Networks now hides the corresponding edges rather than changing their transparency. * Many improvements to the user interface.

3.3.4

Works with Cytoscape 3.0

Release Notes

* Fixed issue with re-saving previously saved sessions ("duplicate entry" error)

3.3.3

Works with Cytoscape 3.0

Release Notes

* Fixed issues with loading previously saved sessions * Fixed bug where missing values in the last column of an imported profile causes a crash

3.3.2

Works with Cytoscape 3.0

Release Notes

* Added support for proxies * Fixed issues when importing networks using a locale where the decimal point is not the period character

3.3.1

Works with Cytoscape 3.0

Release Notes

* Fixed issues with file selection on Mac OS X

3.3

Works with Cytoscape 3.0

Release Notes

* First universal JAR release: works on Cytoscape 2.6+ and 3.0+, as well as command line * Simplified command line tool syntax * Fixed bug in Cross Validator involving user imported data

3.2.1

Works with Cytoscape 3.0

Release Notes

Fixed startup issue involving a very unhelpful error message.

3.2.0

Works with Cytoscape 3.0

Release Notes

First official release for Cytoscape 3.0.

3.0.0.beta2

Works with Cytoscape 3.0

Release Notes

This is a sneak preview of the first release of the GeneMANIA plugin for Cytoscape 3.0.

3.0.0.beta1

Works with Cytoscape 3.0

Release Notes

This is a sneak preview of the first release of the GeneMANIA plugin for Cytoscape 3.0.

CYTOSCAPE 3

Version 3.4.1

License Click here

Released 24 May 2016

Works with Cytoscape 3.3

Download Stats Click here

CYTOSCAPE 2

Version 3.3

Released 6 Nov 2013

Works with Cytoscape 2.6, 2.7, 2.8

Download Stats Click here