EnrichmentMap: AutoAnnotate greyed out

[Shraddha Pai]

Hi, I'm running Cytoscape 3.10.2 with EnrichmentMap v3.5.0 installed.

I just generated a network using gProfiler, but the option to use AutoAnnotate to Find Clusters is greyed out (see screenshot). Am I missing a step?

Per the app store, AutoAnnotate should have come bundled with the EnrichmentMap app. I also separately tried downloading the AutoAnnotate jar file but wasn't sure what the latest way to install it was.

Thank you in advance,

Shraddha

[Mike Kucera]

Hi Shraddha,

AutoAnnotate is not installed automatically when installing just EnrichmentMap. 

If you install the "EnrichmentMap Pipeline Collection" then that will install EnrichmentMap, AutoAnnotate, WordCloud and clusterMaker2. 

https://apps.cytoscape.org/apps/enrichmentmappipelinecollection

It's also recommended to install the "yFiles layout algorithms" app because the yFiles organic layout is now the default layout when creating an EM network.

The easiest way to install an app is to first start Cytoscape, then go to the app store page for the app, then click the "Install" button. If Cytoscape is running it will install it in the right place automatically.

To manually install an app jar file that you downloaded, copy it to the <user-home>/CytoscapeConfiguration/3/apps/installed folder.

Hope that clears things up.

Mike.

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[Shraddha Pai]

Hi Mike,

Yes, that helped - I installed the Pipeline collection and was able to successfully use AutoAnnotate thereafter.

Thank you,

Shraddha

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