patpy.datasets.stephenson

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patpy.datasets.stephenson#

patpy.datasets.stephenson(kind='processed', overwrite=False, return_dataset_info=False)#

Multi-omics immune response in COVID-19 (Stephenson) dataset.

The processed version was prepared with the standard scanpy pipeline; cells annotated as “nan” were removed; PCA, scVI, scANVI, and scPoli dimensionality reduction were applied. The dataset contains 639,482 cells and 3,000 features. The processed download is approximately 1.5 GB compressed and ~4.5 GB unzipped.

Parameters:

  • kind (Literal['raw', 'processed'] (default: 'processed')) – Either "processed" (default) or "raw". Currently only "processed" is available; "raw" raises NotImplementedError.

  • overwrite (bool (default: False)) – If True, re-download the dataset even when a cached copy exists.

  • return_dataset_info (bool (default: False)) – If True, return a tuple (adata, DatasetInfo) instead of just adata.

References

Stephenson, E., Reynolds, G., Botting, R. A., Calero-Nieto, F. J., Morgan, M. D., Tuong, Z. K., … & Haniffa, M. (2021). Single-cell multi-omics analysis of the immune response in COVID-19. Nature medicine, 27(5), 904-916. https://doi.org/10.1038/s41591-021-01329-2

Return type:

AnnData | tuple[AnnData, DatasetInfo]

Returns:

AnnData object of scRNA-seq profiles, optionally paired with a DatasetInfo describing the dataset’s standard schema.

Examples

>>> import patpy
>>> adata = patpy.datasets.stephenson()
>>> adata, info = patpy.datasets.stephenson(return_dataset_info=True)
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