Including quality covariates

[Polina M]

Dear authors,

Thank you for the nice paper! I am trying to run the pipeline on K562 cells, and I wanted to include quality covariates which according to Figures 2I and S2A-C contribute greatly to the variance explained by the model (the contribution is larger than of perturbations or cell states). Could you please direct me to:

1. a section in the paper that describes how exactly you included "quality covariates"

2. corresponding python code at the github folder where this is implemented

Best regards,

Polina Suter