What’s New¶

Release Notes¶

Better support for AutoAnnotate summary networks. They now work with the Heat Map panel.
‘enrichmentmap mastermap’ command now has an argument for the GREAT filter.
Bug fixes.

Created an options menu next to the Data Set list and moved all the buttons that used to be next to the Data Set list into this menu.
Added ability to synchronize data set list with network selection.
Creating a subnetwork from an EnrichmentMap network will copy the EnrichmentMap data to the subnetwork.
Bug fixes.

An EnrichmentMap network can now be created from a STRING or GeneMania network.
The colors used in the ‘Color by DataSet’ chart can be customized.
It is no longer a strict error when gene sets are missing from the GMT file. The user may choose to continue to create the network without the missing gene sets.
The Heat Map panel can sort ranks automatically based on the leading edge.
The Heat Map panel can filter Data Sets based on node/edge selection.
The “Color by DataSet” chart is now filtered based on the selected Data Sets.
Support for importing Enrichr files when creating an EnrichmentMap netwwork.
New ‘Create Command’ button in the Create EnrichmentMap Dialog shows equivalent command for automation.
Bug Fixes

Requires Cytoscape 3.7
Integration with other analysis tools:
- GeneMania
- STRING
- Pathway Commons
New commands for automating EnrichmentMap through CyREST.
- Export PDF
- Set chart options
- Show abd hide datasets
- Create an EM network from data in a table
Column names are now prefixed with “EnrichmentMap::” to take advantage of the column namespace feature added to Cytoscape 3.7.
Bug fixes

Requires Cytoscape 3.5.1
Redesigned Post-Analysis UI
- Ability to preview signature gene sets before import
- Ability to import GMT files from the web (download.baderlab.org)
New Chart: Color by DataSet.
Support for g:profiler 2-phenotype analysis.
Heat Map: Compress expressions by class.
Export Legend to PDF.
Export Heat Map to PDF.
Ability to specify the name of the EnrichmentMap network.
Drag-and-Drop folders onto the Create EnrichmentMap Dialog.
Bug fixes

EnrichmentMap 3.0 is a major release, with the following new features:

Requires Cytoscape 3.4
EnrichmentMap networks can now be created from any number of enrichment data sets (EnrichmentMap 2.0 supported maximum 2 data sets).
New chart visualizations on nodes for visualizing NES scores, p-values or q-values. Three new charts are available: radial heat-map, linear heat-map and heat-strips.
New network creation dialog has the ability to scan a folder for files belonging to each dataset. In most cases this removes the need to manually enter the required files.
New control panel allows the contents and style of the network and charts to be updated dynamically.
New legend dialog.
New streamlined HeatMap panel has the ability to summarize expression data.
Several new commands that allow EnrichmentMap to be automated from external scripts and CyREST.
Bug fixes