stereoAlign.alignment.scgen_alignment

stereoAlign.alignment.scgen_alignment(adata: AnnData, batch_key, cell_type, epochs=200, hvg=None, **kwargs)

scGen wrapper function

Based on scgen with parametrization taken from the tutorial notebook.

Parameters:

• adata – preprocessed anndata object

• batch_key – 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