Automating EnrichmentMap

EnrichmentMap provides several commands which allow basic features to be automated via scripts, the command line or REST.

CyREST App

To call commands via REST the CyREST App is required. CyREST is normally installed by default.

CyRest is updated often. There are two ways to install the latest version:

  1. App Manager

    Open the App Manager dialog from the main menu at Apps > App Manager. Then go to the Check For Updates tab. If there is a newer version available it will be listed.

  2. App Store

    CyRest can also be installed or updated from the App Store Website

Command Documentation

CyREST Documentation

On-line documentation for EnrichmentMap commands can be accessed from the main menu at Help > Automation > CyREST Command API. This will open a web browser with documentation for all the commands that are available through CyREST. Navigate to the enrichmentmap entry and expand it for detailed documentation on each command.

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Note

For more details on using CyRest see the CyREST Documentation

Command Line Dialog Documentation

Open the Command Dialog from the main menu at Tools > Command Line Dialog.

Type help enrichmentmap to list the available commands provided by EnrichmentMap. To get help on a particular command type, for example the build command, type help enrichmentmap build.

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Note

For more details on the Command Line Dialog see the Cytoscape User Docs