How to use lvm-DE


I would like to give a try to lvm-DE for my analyses.
But unfortunately, I couldn’t find documentation neither a function.

Any advice would be appreciated!


Hi, please see this thread for more information.

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Thank you for your prompt answer!
Trying to set up the weight parameter in an into an issue:
TypeError: get_bayes_factors() got an unexpected keyword argument ‘weights’

I am on sci-tools 0.20.3

do you have any idea how I could fix this

I am using this command:

de_df = model.differential_expression(
groupby=“leiden_scVI”, weights=‘importance’,
delta=None, fdr_target=0.01,


So I managed to make it works using the beta version :
pip install scvi-tools==1.0.0-beta.0 --force-reinstall