*This App is part of the [https://apps.cytoscape.org/apps/enrichmentmappipelinecollection EnrichmentMap Collection].*
Finds clusters and visually annotates them with labels and groups. These visualizations provide a concise visual summary which is helpful for network analysis and interpretation.
Features:
* Automates running clusterMaker2 to generate clusters. (Or provide your own clusters by selecting any node attribute.)
* Automatically generates cluster labels based on word frequencies of selected attributes.
* Manages multiple “Annotation Sets” and easily switches between them.
* Change the look of the annotations using several display options.
* Cluster-aware layouts.
* Automatically group and collapse clusters. Creates a simplified view by collapsing each cluster into a “meta-node” and collapsing edges between clusters into a single “meta-edge”.
* Allows to manually create and update clusters.
* Originally designed and used to annotate Enrichment Maps but applicable to any type of network including PPI, pathways, or Social networks.
Warning
> Versions of AutoAnnotate prior to version 1.3.3 are not fully compatibile with Cytoscape 3.8.
> If you are having issues please upgrade to the latest version.
Warning
> Versions of AutoAnnotate prior to version 1.3.0 are incompatible with the latest version of
> clusterMaker2. If you are having issues running AutoAnnotate please upgrade to the latest
> version.
Links:
* [http://autoannotate.readthedocs.io User Guide]
* [http://f1000research.com/articles/5-1717/v1 F1000 Research Software Tool Article]
* [https://github.com/BaderLab/AutoAnnotateApp Code Repository]
[](https://doi.org/10.5281/zenodo.883467)
