AutoAnnotate: User Guide
Overview
AutoAnnotate is a Cytoscape App that 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.
AutoAnnotate started as a feature of the EnrichmentMap App but has since been extracted into its own standalone App.
Getting Started
Requirements
- Java 8
- Cytoscape minimum version 3.3
WordCloud minimum version 3.1.0
- clusterMaker2 minimum version 0.9.5
Installation
- Install Cytoscape
If you don’t have Cytoscape please download the latest release from http://www.cytoscape.org/download.php and install it on your computer.
Install AutoAnnotate
- Open Cytoscape
In the main menu select Apps > App Manager
In the App Manager select AutoAnnotate in the list of All Apps and click the Install button.
The WordCloud app will also be installed automatically along with AutoAnnotate
- Install clusterMaker2 (optional, but highly recommended)
- In the App Manager select clusterMaker2 in the list of All Apps and click the Install button.
Alternatively AutoAnnotate and clusterMaker2 can be installed from the App Store website.
AutoAnnotate on the App Store:
clusterMaker2 on the App Store: http://apps.cytoscape.org/apps/clustermaker2
