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BaderLab / Cytoscape_workflows

collection of notebooks with different cytoscape workflows
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Working with EnrichR results? #6

Open Yaseswini opened 3 years ago

Yaseswini commented 3 years ago

Hi,

The cytoscape plugin hints that we could use the outputs from EnrichR( https://maayanlab.cloud/Enrichr/ ) . I was wondering if there is a tutorial on how get the gmt files from EnrichR and how to use the outputs for enrichment Map ?

Thanks Yaseswini

risserlin commented 3 years ago

I really thought we had a tutorial for Enrichr. It has been on our to do list for a while. Sorry about that. There is an exercise/tutorial here - https://baderlab.github.io/CBW_Pathways_2021/regulatory-network-lab.html#exercise-3.-use-enrichr-with-the-prostate-gene-list. Let me know if you have any specific questions. Thanks, Ruth

risserlin commented 3 years ago

I just noticed that this question is on the cytsocape workflows as opposed to the enrichment map github. Are you looking for an automated way to use enrichr from R?

Yaseswini commented 3 years ago

Thanks, @risserlin !! I am using the R package "enrichr" and i have the results from my analysis. I was just wondering if there is a tutorial on how to obtain the gmt File required for the Enrichment Map.

risserlin commented 3 years ago

A gmt file is not required. It is definitely beneficial to have one but if your generic output results file contains the list of genes as the final column you can run Enrichment map without the gmt file.
You can download the Enrichr gmt files from here - https://maayanlab.cloud/Enrichr/#stats Unfortunately there isn't one file that contains them all (but you might be able to download them in R with wget)

Yaseswini commented 3 years ago

Yea - I just realized that a gmt File isn't required for EnrichR's result. I didn't catch that earlier. Thanks @risserlin - this helps!! Appreciate your quick reply :)