Question

Using R for EnrichR analysis

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Nithisha ▴ 10

@nithisha-14272

Last seen 6.8 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 • 8.9k views

ADD COMMENT • link updated 7.1 years ago by thokall ▴ 160 • written 7.2 years ago by Nithisha ▴ 10

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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

ADD REPLY • link 7.1 years ago Gordon Smyth 52k

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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!

ADD REPLY • link updated 7.1 years ago by Gordon Smyth 52k • written 7.1 years ago by Nithisha ▴ 10

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An alternative would be to use the Enrichr web interface.

ADD REPLY • link 7.1 years ago Gordon Smyth 52k

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Thank you Gordon, I shall try that!

ADD REPLY • link 7.1 years ago Nithisha ▴ 10

score 2 · Accepted Answer · 2017-11-04

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thokall ▴ 160

@thokall-14310

Last seen 11 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