• Heat Map panel usability improvements.
• New option in EnrichmentMap Create dialog for running AutoAnnotate.
• Bug fixes.

• New column, style mapping and chart for -log10(pvalue).
• Better support for latest version of AutoAnnotate.
• Default layout is now yFiles organic layout.
• UI changes to the EnrichmentMap create dialog.
• Bug fixes.

• Fixes a bug where the leading edge was not being rendered correctly in the heat map.

• The Heat Map works for AutoAnnotate summary networks created from EnrichmentMap networks.
• New option to set edge color for multi-dataset networks.
• 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.
• Bug fixes.

• Creating a subnetwork from an EnrichmentMap network will copy the EnrichmentMap data to the subnetwork.
• Bug fixes.

• Bug fixes.

• Enhancements to 'build-table' command for app interoperability.
• Bug fixes.

New in EnrichmentMap 3.3:

• 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.
• Support for importing Enrichr files when creating an EnrichmentMap network.
• New "Create Command" button in the Create Enrichment Map Dialog shows equivalent command for automation.
• New "Getting Started" section on the Create Enrichment Map Dialog to better help new users.
• An EnrichmentMap network can now be created from a STRING or GeneMania network.
• Bug Fixes

Minor features and bug fixes.

• The Heat Map panel is now synchronized with the data set list in the Control Panel. When a data set is disabled the genes/expressions from that data set will be hidden in the Heat Map. This is consistent with how the data set list interacts with the network.
• Added better documentation for commands (accessible via command line or swagger)
• Added 'pattern' argument to mastermap command.
• Bug fixes

• Integration with other tools
  • GeneMANIA
  • STRING
  • Pathway Commons
• New Commands
  • export pdf
  • set chart options
  • show/hide datasets
  • create EM from data in a table (allows EM to be created from STRING)
• New Column name prefixes (EnrichmentMap::name)
  • Uses new Column Namespace feature introduced in Cytoscape 3.7
• Scroll bar in main panel
• Empty ranks always sorted to bottom of heat map
• Drag and drop files onto the creation dialog
• Many bug fixes
• Requires Cytoscape 3.7

• 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.
• Several bug fixes (https://github.com/BaderLab/EnrichmentMapApp/milestone/7?closed=1)
• Requires Cytoscape 3.5.1

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

• 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 fix release

Bug Fixes

• Bug fixes listed here: https://github.com/BaderLab/EnrichmentMapApp/issues?q=is%3Aissue+is%3Aclosed+milestone%3A2.2_release

Features:

• New color scheme for network style.
• Updated the UI to be cleaner and more modern looking.
• Improved the performance of the gene-set similarity calculation, and made the task cancellable.

Bug fixes and Added features in 2.1.0:

Bug fixes:

• Numerous bug fixes that are outlined here: https://github.com/BaderLab/EnrichmentMapApp/issues?q=is%3Aissue+is%3Aclosed+milestone%3A2.1_release

Features:

• Revamped post analysis interface and functionality.   
• Post analysis can be run in known signature mode or signature discovery mode.  Known signature mode calculates post analysis edges for a small subset of sets.  Signature discovery mode allows for filtering of large set of potential signatures to help uncover most likely set.
• Post analysis edges can be calculated using a two sided or one sided Mann whitney test using rank files from either dataset1 or dataset2 separately.  For example, this allows the user to look for pathways that contain a significant set of up-regulated miR targets only.  
• Update g:profiler support so we no longer require a gmt file to be specified.
• Add the ability to specify the set of genes associated with the geneset in the generic enrichment file.
• Added “publication ready” button to legend panel so users can easily toggle between figure ready and normal view of network. 

Bug Fixes and Added features in 2.0.1

Bug Fixes
* Fixed issue with building a two dataset network using edb or rpt because a missing reference to gmt file.
* Fixed rank file load through heatmap panel
* Added error message to say that PDF export is currently not available
* Fixed issue creating heatmap with hiearchical clusters for some datatypes
* Enabled input panel to be reopened after closed by the user.
Fixed issue with GREAT file import(if a line was missing genes it would truncate the load and only load results prior to the line with missing genes)
* GREAT export loads from TSV file instead of a TXT version of the TSV file downloaded.
* Enable GMT only EM creation
* Fixed issue with EM created from all genesets if nothing passed the thresholds

Features
* Enabled EM creation from Bingo 3.0 output files.
* P-value and Q-value can be set using precision of 10-12 or using scientific notation (no limit with scientific notation).
* Added the ability to specify which p-value you want to filter by (hyper, binom, both or either) for GREAT results.
* Enabled slliders to work with precision higher than 10-3. Now works for whatever the cutoff is with an additional range of precision 10-3 less than the cutoff value.