cicero across samples

[AnjaliC4]

Hi, thanks for this awesome tool!

I was wondering how can I combine multiple samples before creating a gene activity matrix using cicero? And store the sample info in metadata.

Also if I were to correct for batch effects, should I do that before creating gene activity matrix and cell-type annotation?

Thanks!! Anjali

[hpliner]

Hello, Check out the monocle3 function combine_cds, I think it should do what you're looking for.

For batch, the gene activity calculation does not take into account dimensionality reduction, etc, so doing batch correction won't change the outcome.

Best, Hannah

[hpliner]

Going to go ahead and close. Reopen if you have further issues