Method to deal with batch effects?

[lucygarner]

I have two datasets where the same experiment was performed on different occasions (experiment was repeated to increase the number of donors). There is a clear batch effect between the datasets. Ideally, I would perform pySCENIC for the two datasets together. However, when I do this with raw counts, the batch effect can be observed in the AUCell scores.

Is there any way to deal with batch effects using pySCENIC or to integrate results from two runs of pySCENIC?