Using R for EnrichR analysis
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Nithisha ▴ 10
@nithisha-14272
Last seen 6.1 years ago

Hi everyone,

Is there a specific package I can utilize in R to conduct EnrichR analysis for up-regulated  and down-regulated genes? While searching I have come across Python packages to do this but not in R. Any advice would be appreciated!

Thanks

Enrichr • 7.7k views
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What do you mean by "EnrichR"? As far as I know, there is no statistical method or software package of that name and capitalization as far as I know.

If you just mean gene ontology or KEGG pathways analysis of DE genes, you could look at the goana() or kegga() functions of the limma package. These workflows give examples of usage:

https://f1000research.com/articles/5-1408

https://f1000research.com/articles/5-1438

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Hello Gordon,

Thank you for your reply. I meant Enrichr ( http://amp.pharm.mssm.edu/Enrichr ). I think that Python can help get results from Enrichr eg. for a list of upregulated genes from DEG analysis, I can get enriched transcription factors, pathways, ontologies etc. I was wondering if I could do the same in R.

Thanks!

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An alternative would be to use the Enrichr web interface.

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Thank you Gordon, I shall try that!

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thokall ▴ 160
@thokall-14310
Last seen 4 weeks ago
Swedish Museum of Natural History

Hi,

If you are referring to this http://amp.pharm.mssm.edu/Enrichr/.

There seem to be a cran package https://cran.r-project.org/web/packages/enrichR/index.html that provides an interface to these databases

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Hi Thokall,

Thank you for your reply! It is Enrichr that I was talking about!

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