scvi

scib.integration.scvi(adata, batch, hvg=None)

scVI wrapper function

Based on scVI version 0.6.7 (available through conda)

Note

scVI expects only non-normalized (count) data on highly variable genes!

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 as well as an embedding representation of the corrected data