CZ CELLxGENE Discover Census

The cellxgene_census package provides an API to facilitate the use of the CZ CELLxGENE Discover Census. For more information about the API and the project visit the chanzuckerberg/cellxgene-census GitHub repo.

For More Help

For more help, please file a issue on the repo, or contact us at soma@chanzuckerberg.com.

If you believe you have found a security issue, we would appreciate notification. Please send email to security@chanzuckerberg.com.

Development Environment Setup

• Create a virtual environment using venv or conda
• cd to the root of this repository
• pip install -e api/python/cellxgene_census
• To install dependencies needed to work on the experimental portion of the API: pip install -e 'api/python/cellxgene_census[experimental]'.
• pip install jupyterlab
• Test it! Either open up a new jupyter notebook or the python interpreter and run this code:

import cellxgene_census

with cellxgene_census.open_soma() as census:

    cell_metadata = cellxgene_census.get_obs(
        census,
        "homo_sapiens",
        value_filter = "sex == 'female' and cell_type in ['microglial cell', 'neuron']",
        column_names = ["assay", "cell_type", "tissue", "tissue_general", "suspension_type", "disease"]
    )
    cell_metadata

The output is a pandas.DataFrame with over 600K cells meeting our query criteria and the selected columns:

The "stable" release is currently 2023-12-15. Specify 'census_version="2023-12-15"' in future calls to open_soma() to ensure data consistency.

                assay        cell_type                 tissue tissue_general suspension_type disease     sex
0        Smart-seq v4  microglial cell  middle temporal gyrus          brain         nucleus  normal  female
1        Smart-seq v4  microglial cell  middle temporal gyrus          brain         nucleus  normal  female
2        Smart-seq v4  microglial cell  middle temporal gyrus          brain         nucleus  normal  female
3        Smart-seq v4  microglial cell  middle temporal gyrus          brain         nucleus  normal  female
4        Smart-seq v4  microglial cell  middle temporal gyrus          brain         nucleus  normal  female
...               ...              ...                    ...            ...             ...     ...     ...
607636  microwell-seq           neuron          adrenal gland  adrenal gland            cell  normal  female
607637  microwell-seq           neuron          adrenal gland  adrenal gland            cell  normal  female
607638  microwell-seq           neuron          adrenal gland  adrenal gland            cell  normal  female
607639  microwell-seq           neuron          adrenal gland  adrenal gland            cell  normal  female
607640  microwell-seq           neuron          adrenal gland  adrenal gland            cell  normal  female

[607641 rows x 7 columns]

• Learn more about the Census API by going through the tutorials in the notebooks