liana.ds.citeseq_pbmc5k

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liana.ds.citeseq_pbmc5k#

liana.ds.citeseq_pbmc5k()#

Load the processed 10X 5k PBMC CITE-seq data.

The RNA and protein modalities were processed following the muon CITE-seq tutorial (https://muon-tutorials.readthedocs.io/en/latest/cite-seq/1-CITE-seq-PBMC-5k.html).

Return type:

MuData

Returns:

Returns a MuData object with a pre-processed mod['rna'] and mod['prot'] modality, with the cell type annotations of the 3.9k shared cells in mod['rna'].obs['celltype'].

Examples

This downloads ~80MB into scanpy.settings.datasetdir on first call, so it is not run here:

import liana as li

mdata = li.ds.citeseq_pbmc5k()
rna, prot = mdata.mod["rna"], mdata.mod["prot"]

It is the dataset used in the multi-modal ligand-receptor tutorial.

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