New in EnrichmentMap 3.3¶
- 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
New in EnrichmentMap 3.2¶
- Requires Cytoscape 3.7
- Integration with other analysis tools:
- 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
New in EnrichmentMap 3.1¶
- 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
New in EnrichmentMap 3.0¶
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