u/Empty-Option7939

Hello all,

I was wondering if anyone with PySCENIC experience could please provide some advice about best practices to run the program. In particular, if my scRNA data comprises both diseased donors and healthy donors, is it more appropriate to run the program on the combined dataset and then subset AUCell results by donor/disease variable, so that the AUC results are more comparable across cells, or is it more appropriate to run separately on disease and on healthy, so that there is less confounding noise and any disease-related signal will be stronger?

For extra credit - if there is an approach which is more correct, is there a way to demonstrate compellingly that this approach makes the most sense?

Thank you in advance.