omicverse.single.run_liana

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omicverse.single.run_liana#

omicverse.single.run_liana(adata, *, groupby, method='rank_aggregate', key_added='liana_res', inplace=True, **kwargs)[source]#

Run LIANA ligand-receptor inference on an AnnData object.

Parameters:

  • adata – AnnData object used by LIANA.

  • groupby (str) – Observation column with cell-type labels.

  • method (str (default: 'rank_aggregate')) – LIANA method name under liana.mt. Defaults to 'rank_aggregate'.

  • key_added (str (default: 'liana_res')) – Key used to store LIANA results in adata.uns when inplace=True.

  • inplace (bool (default: True)) – Whether to write results back to adata.uns.

  • **kwargs – Forwarded to the selected LIANA method.

Returns:

LIANA result table when inplace=False; otherwise returns adata.

Return type:

pandas.DataFrame or AnnData

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