Scpy

a statsmodels implement based on pytorch

can perform single-cell gene differential expression analysis 1000X faster than R package.

requirements

• pandas
• statsmodels
• torch

usage

basic

import scpy

scpy.fit(x, y, family='poisson', device='cpu', **kwargs)

scpy.fit_batch(X, Y, family='negative_binomial', device='cpu', **kwargs)

Support specifying method, maxiter and other parameters in statsmodels optimizers

parallel

python -m scpy demo.py demo.csv -d 0,1,2,3,4,5,6,7

demo.py

args = {
 'X': X,
 'Y': Y,
 'family': 'negative_binomial',
 'xnames': xnames,
 'yname': yname,
 'kwargs': {}
}

todo

• Currently only supports 'poisson' and 'negative_binomial', add more distributions.
• Fix bug on Hessian matrix inversion.
• Automatically cache x and y in fit_batch.