snapatac2.datasets.pbmc10k_multiome#

snapatac2.datasets.pbmc10k_multiome(modality='RNA', type='h5ad')[source]#

Fetch the 10x Genomics 10k PBMC multiome example dataset.

Use this helper to download and cache the paired RNA and ATAC example data for multiome workflows. RNA is available as h5ad only; ATAC is available as either h5ad or fragments.

Anti-Patterns#

Do NOT request modality="RNA" with type="fragment"; RNA returns the RNA h5ad file regardless of type.

param modality:: Modality to fetch. Use “ATAC” for chromatin accessibility data or “RNA” for gene-expression data.
type modality:: Literal['ATAC', 'RNA']
param type:: ATAC representation to fetch. This parameter is ignored when modality="RNA" because only the RNA h5ad file is available.
type type:: Literal['fragment', 'h5ad']
returns:: Path to the requested cached dataset file.
rtype:: Path

Examples

>>> import snapatac2 as snap
>>> atac_file = snap.datasets.pbmc10k_multiome(modality="ATAC", type="h5ad")
>>> rna_file = snap.datasets.pbmc10k_multiome(modality="RNA")
>>> atac_file.suffix == rna_file.suffix == ".h5ad"
True