Announcing Version 2.2 of The GeneMANIA Cytoscape Plugin for Gene Function Prediction
Jason Montojo
Cytoscape plugin and command line tools. This release includes
numerous bug fixes and a handful of new features. You can install
this new release through Cytoscape's plugin manager. Read below for
more details.
New Features:
* The plugin now provides access to three different types of data sets:
* "-core": Only contains the default selected networks.
* "-open_license": Only contains networks with a non-restrictive license.
* Data sets with no suffix are the same as before.
* It's now possible to distinguish between different networks in the
command line tools by also providing their network type; e.g.
"gi|BIOGRID" and "pi|BIOGRID".
* Node attributes now contain functional enrichment descriptions.
* Both JSON and text formats are now supported when importing search
parameters from the GeneMANIA website.
Bug Fixes:
General:
* Fixed a bug in user-created data sets where descriptions for a gene
from a different organism are displayed instead of the proper
description.
QueryRunner:
* "flat" and "xml" reports no longer scale gene scores by 100.
* "xml" report is no longer missing </network> closing tags.
CrossValidator:
* CrossValidator no longer terminates early if it runs into as many
errors as the number of threads.
* Queries where some nodes are neither labeled positive or negative
are now properly handled.
NetworkAssessor:
* NetworkAssessor no longer crashes for queries where the MANIA
algorithm does not converge.
NetworkImporter:
* Imported networks are no longer marked as "default selected".
Documentation for the command line tools can be found here:
http://pages.genemania.org/tools/
Compatibility:
This release works with Cytoscape 2.6.3+, 2.7, and 2.8. Sessions
created by version 1.0 of the GeneMANIA plugin cannot be loaded fully
by 2.1.