scvi.data.purified_pbmc_dataset

scvi.data.purified_pbmc_dataset(save_path='data/', subset_datasets=None, run_setup_anndata=True)[source]

Purified PBMC dataset from: “Massively parallel digital transcriptional profiling of single cells”.

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

Location to use when saving/loading the data.

subset_datasets : List[str] | NoneOptional[List[str]] (default: None)

index for subsetting the follwing list of datasets which are used to form the PurifiedPBMCDataset: “cd4_t_helper”, “regulatory_t”, “naive_t”, “memory_t”, “cytotoxic_t”, “naive_cytotoxic”, “b_cells”, “cd4_t_helper”, “cd34”, “cd56_nk”, “cd14_monocytes”.

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 label info (.obs['labels'])

Examples

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