Extracting genes from scpa ouput

jackbibby1 / SCPA

R package for pathway analysis in scRNA-seq data

https://jackbibby1.github.io/SCPA/

GNU General Public License v3.0

56 stars 5 forks source link

Open cdkodira opened 1 month ago

cdkodira commented 1 month ago

Is there a way to extract genes from the scpa output? thanks

jackbibby1 commented 1 month ago

Hi,

Are you wanting to extract genes from the pathways?

You can do this in msigdbr something like:

msigdbr("Homo sapiens", "H") %>%
   filter(gs_name == "HALLMARK_COMPLEMENT") %>%
   pull(gene_symbol)

If you want to know specific genes driving the signature then I'll direct you to the discussion here and the links I mentioned

Jack