harmony

scib.integration.harmony(adata, batch, hvg=None, **kwargs)

Harmony wrapper function

Based on harmony-pytorch version 0.1.7

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