annotate

hnoca.snapseed.annotate.annotate(adata, marker_dict, group_name, layer=None, **kwargs)

Annotate clusters based on a manually defined cell type markers.

Parameters:

Name	Type	Description	Default
adata	AnnData	AnnData object	required
marker_dict	dict	Dict with marker genes for each celltype	required
group_name	str	Name of the column in adata.obs that contains the cluster labels	required
layer	str | None	Layer in adata to use for expression	None
**kwargs		Additional arguments to pass to the annotation function.	{}

Returns

pd.DataFrame with assignments