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Question: Using R for EnrichR analysis
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gravatar for Nithisha
18 days ago by
Nithisha0
Nithisha0 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 17 days ago by thokall60 • written 18 days ago by Nithisha0

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 17 days ago • written 17 days ago by Gordon Smyth32k

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 17 days ago by Gordon Smyth32k • written 17 days ago by Nithisha0
1

An alternative would be to use the Enrichr web interface.

ADD REPLYlink modified 17 days ago • written 17 days ago by Gordon Smyth32k

Thank you Gordon, I shall try that!

ADD REPLYlink written 16 days ago by Nithisha0
2
gravatar for thokall
17 days ago by
thokall60
Uppsala University
thokall60 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 17 days ago by thokall60

Hi Thokall,

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

ADD REPLYlink written 17 days ago by Nithisha0
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