Region set, scores.feather and NameError: name 'run_cgs_models_mallet about scenicplus HOT 3 OPEN

Hi @strawberry098

Yes you will need both, please see: https://scenicplus.readthedocs.io/en/latest/tutorials.html for more information.
Regarding the NameError: name 'run_cgs_models_mallet' is not defined: Did you install and import pycisTopic?

All the best,

Seppe

from scenicplus.

Hi @SeppeDeWinter

Thanks for the reassurance. I'm new to python, and I realized I didn't import (despite installed) mallet. After importing, the mallet model function ran.

The reason why I opened issue #452 was because after I created the cisTopic object using a 10x Multiome snATAC-seq peak counts matrix, I didn't get the cell annotation info. I realized the peak counts matrix normally does not include cell annotation info, but how can I add it to the cisTopic object?

Thank you!

from scenicplus.

Hi @strawberry098

Please see: https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html#Adding-metadata-to-a-cisTopic-object for how to add cell metadata to your cisTopic object.

Seppe

from scenicplus.