EnrichmentMap

Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.
*This App is part of the [https://apps.cytoscape.org/apps/enrichmentmappipelinecollection EnrichmentMap Collection].* The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network. It will operate on any generic enrichment results as well as specifically on Gene Set Enrichment Analysis (GSEA) results. Nodes represent gene-sets and edges represent mutual overlap; in this way, highly redundant gene-sets are grouped together as clusters, dramatically improving the capability to navigate and interpret enrichment results. Gene-set enrichment is a data analysis technique taking as input: * A (ranked) gene list, from a genomic experiment * Gene-sets, grouping genes on the basis of a-priori knowledge (e.g. Gene Ontology) or experimental data (e.g. co-expression modules) and generating as output the list of enriched gene-sets, i.e. best sets that summarizing the gene-list. It is common to refer to gene-set enrichment as functional enrichment because functional categories (e.g. Gene Ontology) are commonly used as gene-sets. Links: * [https://enrichmentmap.readthedocs.io User Guide] * [https://enrichmentmap.readthedocs.io/en/latest/Automating.html Automation Guide] * [https://github.com/BaderLab/EnrichmentMapApp Code Repository]

3.5.0

Works with Cytoscape 3.7

Release Notes

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

3.4.0

Works with Cytoscape 3.7

Release Notes

* 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.

3.3.6

Works with Cytoscape 3.7

Release Notes

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

3.3.5

Works with Cytoscape 3.7

Release Notes

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

3.3.4

Works with Cytoscape 3.7

Release Notes

* 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.

3.3.3

Works with Cytoscape 3.7

Release Notes

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

3.3.2

Works with Cytoscape 3.7

Release Notes

* Bug fixes.

3.3.1

Works with Cytoscape 3.7

Release Notes

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

3.3.0

Works with Cytoscape 3.7

Release Notes

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

3.2.1

Works with Cytoscape 3.7

Release Notes

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

3.2.0

Works with Cytoscape 3.7

Release Notes

- 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

3.1.0

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

* 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

3.0.0

Works with Cytoscape 3.4

Release Notes

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.

2.2.0

Works with Cytoscape 3.3

Release Notes

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.

2.1.0

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

### 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. 

2.0.1

Works with Cytoscape 3.1

Release Notes

### Bug Fixes and Added features in 2.0.1<BR> **Bug Fixes**<BR> * Fixed issue with building a two dataset network using edb or rpt because a missing reference to gmt file.<BR> * Fixed rank file load through heatmap panel<BR> * Added error message to say that PDF export is currently not available<BR> * Fixed issue creating heatmap with hiearchical clusters for some datatypes <BR> * Enabled input panel to be reopened after closed by the user.<BR> 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)<BR> * GREAT export loads from TSV file instead of a TXT version of the TSV file downloaded.<BR> * Enable GMT only EM creation<BR> * Fixed issue with EM created from all genesets if nothing passed the thresholds<BR><BR> **Features**<BR> * Enabled EM creation from Bingo 3.0 output files.<BR> * P-value and Q-value can be set using precision of 10-12 or using scientific notation (no limit with scientific notation).<BR> * Added the ability to specify which p-value you want to filter by (hyper, binom, both or either) for GREAT results.<BR> * 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.<BR>

2.0.0

Works with Cytoscape 3.1


CYTOSCAPE 3

Version 3.5.0

Released 7 Oct 2024

Works with Cytoscape 3.7

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