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](https://apps.cytoscape.org/apps/stringapp) for a variety of interaction types
- [WikiPathways](https://apps.cytoscape.org/apps/wikipathways) for community-curated pathways
- [ReactomeFI](https://apps.cytoscape.org/apps/reactomefiplugin) for reaction-based pathway models
- [AgilentLiteratureSearch](https://apps.cytoscape.org/apps/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](https://apps.cytoscape.org/apps/clustermaker2) to perform clustering
- [Diffusion](https://apps.cytoscape.org/apps/diffusion) to perform advanced node selection
- [jActiveModules](https://apps.cytoscape.org/apps/jactivemodules) to identify network modules
### Perform Functional Enrichment Analysis
- [stringApp](https://apps.cytoscape.org/apps/stringapp) (GO, KEGG)
- [BiNGO](https://apps.cytoscape.org/apps/bingo) (GO)
- [ENViz](https://apps.cytoscape.org/apps/enviz) (GO, WikiPathways)
### Functional Interpretation and Display
- [EnrichmentMap](https://apps.cytoscape.org/apps/enrichmentmap) for pathway models
- [CyTargetLinker](https://apps.cytoscape.org/apps/cytargetlinker) for adding miRNA, TF and drug interactions
- [CyAnimator](https://apps.cytoscape.org/apps/cyanimator) to animate across time points or comparisons
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***Refer to the documentation and app store pages for each individual app for more details***
