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WhatsNew.rst

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What's New

Release Notes

New in EnrichmentMap 3.5

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

New in EnrichmentMap 3.4

  • 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.

New in EnrichmentMap 3.3.5

  • 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.

New in EnrichmentMap 3.3.4

  • 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.

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:
    • 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

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