scvi.data.heart_cell_atlas_subsampled#
- scvi.data.heart_cell_atlas_subsampled(save_path='data/', remove_nuisance_clusters=True)[source]#
Combined single cell and single nuclei RNA-Seq data of 485K cardiac cells with annotations.
Dataset was filtered down randomly to 20k cells using
subsample()
. The original data can be downloaded from https://www.heartcellatlas.org/#DataSources.- Parameters:
- Return type:
- Returns:
AnnData
Notes
The data were filtered using the following sequence:
>>> adata = anndata.read_h5ad(path_to_anndata) >>> bdata = sc.pp.subsample(adata, n_obs=20000, copy=True) >>> sc.pp.filter_genes(bdata, min_counts=3) >>> bdata.write_h5ad(path, compression="gzip")
Examples
>>> import scvi >>> adata = scvi.data.heart_cell_atlas_subsampled()