How to Access Cell Type Libraries (e.g., Allen Brain Atlas 10x scRNA 2021) via EnrichR in R or Python

[SaraAlidadiani]

Hi,

On the EnrichR website, when I submit a list of genes, I can view enrichment results across various categories such as pathways, ontologies, diseases/drugs, and cell types. I'm particularly interested in the Cell Types results.

I want to replicate this analysis in R or Python by providing a list of genes and querying one of the cell type-related libraries available on EnrichR—for example, "Allen Brain Atlas 10x scRNA 2021".

However, I couldn't find clear documentation on programmatically accessing or using this function and specific library. Could you give me some guidance or examples on how to do this using code?

Looking forward to hearing from your team!
Thanks!
Sara

[ycl6]

Hi @SaraAlidadiani

I think the library you wanted is called Allen_Brain_Atlas_10x_scRNA_2021 as listed here.

If follow the guide on enrichR's home page, you can set dbs to that and run enrichr, e.g.

dbs <- "Allen_Brain_Atlas_10x_scRNA_2021"
enriched <- enrichr(input, dbs)