Hanna

Using the raw UMI matrix as you described is the correct input for scHPF. The "ranked_genes" file orders genes by their per-factor gene scores, which you can think of as...

Glad you have found scHPF useful! You can do a PPC as follows: ```python import numpy as np import schpf # load the model model_file = '/path/to/joblib.joblib' model = schpf.load_model(model_file)...

Hi Jens, Glad you have found scHPF useful! I think how you handle batch effects under the current scHPF model will be highly dataset dependent. In general, I think what...

Glad you enjoyed the paper! A numba implementation with a scikit-learn-like interface is already in the works, which will hopefully address many of the issues you listed. I plan to...

I just merged a numba implementation which may address your concerns. In addition, it is much faster an memory efficient than the previous tensorflow implementation, and has a pretty clear...