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Question: Using R for EnrichR analysis
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gravatar for Nithisha
10 months ago by
Nithisha10
Nithisha10 wrote:

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

ADD COMMENTlink modified 10 months ago by thokall120 • written 10 months ago by Nithisha10

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 REPLYlink modified 10 months ago • written 10 months ago by Gordon Smyth35k

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 REPLYlink modified 10 months ago by Gordon Smyth35k • written 10 months ago by Nithisha10
1

An alternative would be to use the Enrichr web interface.

ADD REPLYlink modified 10 months ago • written 10 months ago by Gordon Smyth35k

Thank you Gordon, I shall try that!

ADD REPLYlink written 10 months ago by Nithisha10
2
gravatar for thokall
10 months ago by
thokall120
Swedish Museum of Natural History
thokall120 wrote:

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

ADD COMMENTlink written 10 months ago by thokall120

Hi Thokall,

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

ADD REPLYlink written 10 months ago by Nithisha10
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