This is a basic but flexible Negative-Binomial regression tool intended for differential expression analysis on single cell count data.
Right now it's mainly a testbed for tinkering with modeling and regressing out various kind of confounding effects.
Basic usage:
from prodx import DEModel
model = DEModel(
adata_osn,
"~ covariate1 * covariate2 + covariate3",
"~ confounder1 + connfounder2",
)
model.fit()
model.de_results("covariate1[T.True]").to_csv("de-results.csv")