| Name | cellxgene-census JSON |
| Version |
1.16.2
JSON |
| download |
| home_page | None |
| Summary | 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/ |
| upload_time | 2024-10-07 19:44:01 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | <3.13,>=3.10 |
| license | MIT |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
|
# 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](https://github.com/chanzuckerberg/cellxgene-census/).
## 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](./src/cellxgene_census/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:
```python
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:
```python
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](../notebooks/)
Raw data
{
"_id": null,
"home_page": null,
"name": "cellxgene-census",
"maintainer": null,
"docs_url": null,
"requires_python": "<3.13,>=3.10",
"maintainer_email": null,
"keywords": null,
"author": null,
"author_email": "Chan Zuckerberg Initiative Foundation <soma@chanzuckerberg.com>",
"download_url": "https://files.pythonhosted.org/packages/f5/3e/5482ec97c597853106172293341e7592fdcea4d1c89f592d0083899a7d49/cellxgene_census-1.16.2.tar.gz",
"platform": null,
"description": "# CZ CELLxGENE Discover Census\n\nThe `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](https://github.com/chanzuckerberg/cellxgene-census/).\n\n## For More Help\n\nFor more help, please file a issue on the repo, or contact us at <soma@chanzuckerberg.com>.\n\nIf you believe you have found a security issue, we would appreciate notification. Please send email to <security@chanzuckerberg.com>.\n\n## Development Environment Setup\n\n- Create a virtual environment using `venv` or `conda`\n- `cd` to the root of this repository\n- `pip install -e api/python/cellxgene_census`\n- To install dependencies needed to work on the [experimental](./src/cellxgene_census/experimental/) portion of the API:\n `pip install -e 'api/python/cellxgene_census[experimental]'`.\n- `pip install jupyterlab`\n- **Test it!** Either open up a new `jupyter` notebook or the `python` interpreter and run this code:\n\n```python\nimport cellxgene_census\n\nwith cellxgene_census.open_soma() as census:\n\n cell_metadata = cellxgene_census.get_obs(\n census,\n \"homo_sapiens\",\n value_filter = \"sex == 'female' and cell_type in ['microglial cell', 'neuron']\",\n column_names = [\"assay\", \"cell_type\", \"tissue\", \"tissue_general\", \"suspension_type\", \"disease\"]\n )\n cell_metadata\n```\n\nThe output is a `pandas.DataFrame` with over 600K cells meeting our query criteria and the selected columns:\n\n```python\n\nThe \"stable\" release is currently 2023-12-15. Specify 'census_version=\"2023-12-15\"' in future calls to open_soma() to ensure data consistency.\n\n assay cell_type tissue tissue_general suspension_type disease sex\n0 Smart-seq v4 microglial cell middle temporal gyrus brain nucleus normal female\n1 Smart-seq v4 microglial cell middle temporal gyrus brain nucleus normal female\n2 Smart-seq v4 microglial cell middle temporal gyrus brain nucleus normal female\n3 Smart-seq v4 microglial cell middle temporal gyrus brain nucleus normal female\n4 Smart-seq v4 microglial cell middle temporal gyrus brain nucleus normal female\n... ... ... ... ... ... ... ...\n607636 microwell-seq neuron adrenal gland adrenal gland cell normal female\n607637 microwell-seq neuron adrenal gland adrenal gland cell normal female\n607638 microwell-seq neuron adrenal gland adrenal gland cell normal female\n607639 microwell-seq neuron adrenal gland adrenal gland cell normal female\n607640 microwell-seq neuron adrenal gland adrenal gland cell normal female\n\n[607641 rows x 7 columns]\n\n```\n\n- Learn more about the Census API by going through the tutorials in the [notebooks](../notebooks/)\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "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/",
"version": "1.16.2",
"project_urls": {
"homepage": "https://github.com/chanzuckerberg/cellxgene-census",
"repository": "https://github.com/chanzuckerberg/cellxgene-census"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "72cd698e57ba5e2780f94dcd1fc0580236b9e5f5be090413316afa2292ee23b5",
"md5": "c7df588a4d3d4ced5308b4aea0c5f2e3",
"sha256": "1a8694fea8ee6a9e93157540b22eddbf59c5b23997b583f08505c4b57d92e3bf"
},
"downloads": -1,
"filename": "cellxgene_census-1.16.2-py3-none-any.whl",
"has_sig": false,
"md5_digest": "c7df588a4d3d4ced5308b4aea0c5f2e3",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": "<3.13,>=3.10",
"size": 54814,
"upload_time": "2024-10-07T19:43:59",
"upload_time_iso_8601": "2024-10-07T19:43:59.726271Z",
"url": "https://files.pythonhosted.org/packages/72/cd/698e57ba5e2780f94dcd1fc0580236b9e5f5be090413316afa2292ee23b5/cellxgene_census-1.16.2-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "f53e5482ec97c597853106172293341e7592fdcea4d1c89f592d0083899a7d49",
"md5": "50c16ebce6bc410f27a16c3a51cd6938",
"sha256": "c007031b1e42b320a191ff1f20ea4099ea935fe5416dffcd710b0e4a94c28ce1"
},
"downloads": -1,
"filename": "cellxgene_census-1.16.2.tar.gz",
"has_sig": false,
"md5_digest": "50c16ebce6bc410f27a16c3a51cd6938",
"packagetype": "sdist",
"python_version": "source",
"requires_python": "<3.13,>=3.10",
"size": 124045,
"upload_time": "2024-10-07T19:44:01",
"upload_time_iso_8601": "2024-10-07T19:44:01.712732Z",
"url": "https://files.pythonhosted.org/packages/f5/3e/5482ec97c597853106172293341e7592fdcea4d1c89f592d0083899a7d49/cellxgene_census-1.16.2.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-10-07 19:44:01",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "chanzuckerberg",
"github_project": "cellxgene-census",
"travis_ci": false,
"coveralls": true,
"github_actions": true,
"lcname": "cellxgene-census"
}
