scgen

scib.integration.scgen(adata, batch, cell_type, epochs=100, hvg=None, **kwargs)

scGen wrapper function

Based on scgen version 2.1.0 with parametrization taken from the tutorial notebook.

Parameters:

  • adata – preprocessed anndata object

  • batch – batch key in adata.obs

  • hvg – list of highly variables to subset to. If None, the full dataset will be used

Returns:

anndata object containing the corrected feature matrix