How to specify species as rat in EnrichR analysis

smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis

https://smorabit.github.io/hdWGCNA/

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How to specify species as rat in EnrichR analysis #175

Closed Ldec12 closed 5 months ago

Ldec12 commented 6 months ago

Hi Your R package is excellent. I have a question. I'm using rat single-cell sequencing data. How can I specify the species as rat in the EnrichR analysis? I appreciate your help.

smorabit commented 5 months ago

Hi, I do not personally have fly data to test this with but I believe that you can run this code:

library(enrichR)

# change the enrichR database
setEnrichrSite("FlyEnrichr")

Then you can run the hdWGCNA function RunEnrichr. Keep in mind that the databases that you include must be part of FlyEnrichr, you can check the list of valid databases here.

smorabit commented 5 months ago

Sorry I just realized that you were talking about rat, not fly. It looks like EnrichR does not have a database for Rat. In that case, you will have to convert your gene names to their human orthologs before running EnrichR. You can get the ortholog information from BioMart.