EnrichmentMap

Visualizes enrichment of specific functions (GO terms) by interactions between functions.
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.

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.

2.2.1

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

Bug fix release

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 3.0.0

Released 5 Sep 2017

Works with Cytoscape 3.4

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CYTOSCAPE 2

Version 1.3

Released 21 Jul 2014

Works with Cytoscape 2.6, 2.7, 2.8

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