, rna_anndata=None, atac_anndata=None, modality_key='modality')[source]#

Concatenate multiome and single-modality input anndata objects. These anndata objects should already have been preprocessed so that both single-modality objects use a subset of the features used in the multiome object. The feature names (index of .var) should match between the objects.

multi_anndata : AnnData

AnnData object with Multiome data (Gene Expression and Chromatin Accessibility)

rna_anndata : AnnData | NoneOptional[AnnData] (default: None)

AnnData object with gene expression data

atac_anndata : AnnData | NoneOptional[AnnData] (default: None)

AnnData object with chromatin accessibility data

modality_key : str (default: 'modality')

The key to add to the resulting AnnData .obs, indicating the modality each cell originated from. Default is “modality”.


Features that exist in either rna_anndata or atac_anndata but do not exist in multi_anndata will be discarded.

Return type:



An AnnData object with all cells in the input objects