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Release History

Categories: automation, enrichment analysis, gene function prediction, network generation

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. - Supports *Cytoscape Automation* (e.g. search GeneMANIA from Python and R workflows).

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3.5.3

Works with Cytoscape 3.9

Release Notes

* Fixes empty file when exporting the results from an online search. * Fixes error when importing an organism from a text file. * Fixes issue where the progress dialog appears behind the other dialogs when installing an organism data.

3.5.2

Works with Cytoscape 3.7

Release Notes

* Fixes bug where the GeneMANIA Data Sets dialog would be displayed every time a Cytoscape session was loaded if no dataset was installed. * Fixes bug where networks from "online" searches would not be reloaded properly if the cytoscape session had results from both local and online searches. * A few UI improvements and fixes, mostly for Cytoscape 3.8.

3.5.1

Works with Cytoscape 3.6

Release Notes

* Increases the HTTP Client's default read timeout from 10 sec to 4 min, which should fix the 'timeout' error on remote queries that return large networks. * Also, users can now change the timeout value through the GeneMANIA Preferences property *search.timeout.seconds*.

3.5.0

Works with Cytoscape 3.6

Release Notes

* Adds GeneMANIA provider to Cytoscape's *Network Search Bar* (online search, no data download required). * Adds support for *Cytoscape Automation* (`search` and `organims` commands) * A few UI improvements. * Minor bug fixes.

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