API to facilitate the use of the CZ CELLxGENE Discover Census. For more information about the API and the project visit https://github.com/chanzuckerberg/cellxgene-census/
Project description
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
venvorconda cdto the root of this repositorypip 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
jupyternotebook or thepythoninterpreter and run this code:
import cellxgene_census
with cellxgene_census.open_soma() as census:
# Reads SOMADataFrame as a slice
cell_metadata = census["census_data"]["homo_sapiens"].obs.read(
value_filter = "sex == 'female' and cell_type in ['microglial cell', 'neuron']",
column_names = ["assay", "cell_type", "tissue", "tissue_general", "suspension_type", "disease"]
)
# Concatenates results to pyarrow.Table
cell_metadata = cell_metadata.concat()
# Converts to pandas.DataFrame
cell_metadata = cell_metadata.to_pandas()
print(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
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