cellxgene-census 1.16.1

Description:

cellxgenecensus 1.16.1

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