dotools_py.dt.example_10x

Contents

dotools_py.dt.example_10x#

dotools_py.dt.example_10x(path='/tmp/dotools_datasets/')[source]#

Download 10X datasets.

Downloads a dataset of PBMC from healty and malignant B cells. Two H5 files will be downloaded (raw_feature_bc_matrix.h5) and (filtered_feature_bc_matrix.h5) for each condition (healthy and disease). They will be saved following the structure output from CellRanger (e.g., healhty/outs/*.h5 or disease/outs/*.h5).

Parameters:
path str | Path (default: '/tmp/dotools_datasets/')

Path where the data is downloaded. Two subfolders will be created.

Return type:

None

Returns:

Returns None. H5 files are saved under the provided path. For each condition a subfolder will be created in the provided path.

Example

>>> import dotools_py as do
>>> import scanpy as sc
>>> do.dt.example_10x("/tmp/dotools_datasets/")
2025-10-22 13:29:52,730 - Downloading data to /tmp/dotools_datasets/
Downloading healthy filtered: 100%|██████████| 20.8M/20.8M [00:00<00:00, 97.5MiB/s]
Downloading healthy raw: 100%|██████████| 147M/147M [00:01<00:00, 88.1MiB/s]
Downloading disease filtered: 100%|██████████| 18.7M/18.7M [00:00<00:00, 104MiB/s]
Downloading disease raw: 100%|██████████| 144M/144M [00:01<00:00, 85.1MiB/s]
>>> adata = sc.read_10x_h5("/tmp/dotools_datasets/healthy/outs/filtered_feature_bc_matrix.h5")
>>> adata
AnnData object with n_obs × n_vars = 7865 × 33538
var: 'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'
Contents