scvi.data.pbmcs_10x_cite_seq

scvi.data.pbmcs_10x_cite_seq(save_path='data/', protein_join='inner', run_setup_anndata=True)[source]

Filtered PBMCs from 10x Genomics profiled with RNA and protein.

Datasets were filtered for doublets and other outliers as in https://github.com/YosefLab/totalVI_reproducibility/blob/master/data/data_filtering_scripts/pbmc_10k/pbmc_10k.py

Parameters
save_path : strstr (default: 'data/')

Location to use when saving/loading the data.

protein_join : strstr (default: 'inner')

Whether to take an inner join or outer join of proteins

run_setup_anndata : boolbool (default: True)

If true, runs setup_anndata() on dataset before returning

Return type

AnnDataAnnData

Returns

AnnData with batch info (.obs['batch']), and protein expression (.obsm["protein_expression"])

Missing protein values are zero, when protein_join == "outer and are identified during AnnData setup.

Examples

>>> import scvi
>>> adata = scvi.data.pbmcs_10x_cite_seq()