Functional Enrichment Collection

Collection of apps to facilitate functional enrichment analysis. By installing this app, you will be installing a set of apps.
This collection of apps has been made to facilitate functional enrichment analysis. By installing this app, you are installing the following set of apps that work well together in workflows like this: ### Retrieve Networks and Pathways Starting with a gene list based on your omics experiment, for example, you can retrieve interactions or pathways using the following apps in this collection to generate a network: - **stringApp** for a variety of interaction types - **GeneMANIA** for a variety of interaction types (or [via website](http://genemania.org)) - **WikiPathways** for community-curated pathways - **ReactomeFI** for reaction-based pathway models - **AgilentLiteratureSearch** based on co-occurrence in abstracts ### Integrate and Explore Your Data - Import your omics data into Cytoscape - Use built-in ID mapping via right-click on column header (if needed) - **clusterMaker2** to perform clustering - **Diffusion** to perform advanced node selection - **jActiveModules** to identify network modules ### Perform Functional Enrichment Analysis - **stringApp** (GO, KEGG) - **BiNGO** (GO) - **ENViz** (GO, WikiPathways) ### Functional Interpretation and Display - **EnrichmentMap** for pathway models - **CyTargetLinker** for adding miRNA, TF and drug interactions - **CyAnimator** to animate across time points or comparisons --- ***Refer to the documentation and app store pages for each individual app for more details***

3.0

Works with Cytoscape 3.5


2.0

Works with Cytoscape 3.3


1.0

Works with Cytoscape 3.3


CYTOSCAPE 3

Version 3.0

Released 11 Aug 2017

Works with Cytoscape 3.5

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