Open SaraAlidadiani opened 2 days ago
Hi @SaraAlidadiani There's a discussion about this in https://github.com/wjawaid/enrichR/issues/67. Short answer is, the current stable version of enrichR doesn't have the option to add background genes in the enrichment analysis.
You can do this on the Enrichr website https://maayanlab.cloud/Enrichr/, or you can follow #67 on how to install and use a revised version of enrichR (PR https://github.com/wjawaid/enrichR/pull/72) that supports a background.
Thank you for your prompt response. Following the https://github.com/wjawaid/enrichR/issues/67 I could use background. Could you also please share how we can visualize the pathways with this one? I couldn't use the same way for visualization when I was using the enrichR package without a background version. Many thanks!
Hi @SaraAlidadiani The colname of the output is probably slightly different, that could be the reason why the existing plot function is not recognise the input format. I'll have a look in the next week or so and suggest a fix.
Hello,
I am using Enrichr in "R" for my pathway analysis. It is not references in the package description https://cran.r-project.org/web/packages/enrichR/enrichR.pdf how to define the background in R.
Is it possible to share how we can provide background to do enrichR pathway analysis in R and add this option in the documentation, please?
I am writing the code that I used, but I couldn't figure out how to add the list of my background genes.
Thanks you!