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 `_