many thanks for integrating CellAssign into the scvi unisverse! I got cell ontology terms and marker genes from cell taxonomy (Cell Taxonomy: a curated repository of cell types with multifaceted characterization | Nucleic Acids Research | Oxford Academic) and summarized the CL tags by cell types of interest.
I have 125802 10x cells from patient. My marker gene matrix is 522 genes of 20 cell types. I setup with categorical covariates (patient ID etc.) and use 48 CPU.
My problem is that for max_epoche=10 it takes scvi about 45 min to finish. Am I doing something wrong or is that rather long run time expected? Maybe I missed it but is there a parameter to speed up CellAssign in scvi?
Many thanks for your help!