Metadata-Version: 2.4
Name: ehrdata
Version: 0.0.3
Summary: A Python package for EHR data
Author: Eljas Roellin, Lukas Heumos, Xinyue Zhang
Maintainer-email: Eljas Roellin <eljas.roellin@helmholtz-munich.de>, Lukas Heumos <lukas.heumos@posteo.net>
Requires-Python: >=3.11,<3.14
Description-Content-Type: text/markdown
License-Expression: Apache-2.0
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
License-File: LICENSE
Requires-Dist: anndata
Requires-Dist: duckdb
Requires-Dist: filelock
Requires-Dist: lamin-utils
Requires-Dist: requests
Requires-Dist: rich
Requires-Dist: session-info2
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Requires-Dist: pre-commit ; extra == "dev"
Requires-Dist: twine ; extra == "dev"
Requires-Dist: docutils>=0.8,!=0.18.*,!=0.19.* ; extra == "doc"
Requires-Dist: ehrdata[torch, lamin, vitessce] ; extra == "doc"
Requires-Dist: ipykernel ; extra == "doc"
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Requires-Dist: sphinxcontrib-bibtex>=1 ; extra == "doc"
Requires-Dist: sphinxext-opengraph ; extra == "doc"
Requires-Dist: ehrapy ; extra == "ehrapy"
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Requires-Dist: omop ; extra == "lamin"
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Requires-Dist: ehrdata[torch, vitessce, lamin] ; extra == "test"
Requires-Dist: pytest ; extra == "test"
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Requires-Dist: vitessce[all]>=3.4 ; extra == "vitessce"
Requires-Dist: zarr>=2.18.7,<3 ; extra == "vitessce"
Project-URL: Documentation, https://ehrdata.readthedocs.io/
Project-URL: Homepage, https://github.com/theislab/ehrdata
Project-URL: Source, https://github.com/theislab/ehrdata
Provides-Extra: dev
Provides-Extra: doc
Provides-Extra: ehrapy
Provides-Extra: lamin
Provides-Extra: test
Provides-Extra: torch
Provides-Extra: vitessce

# ehrdata

[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/ehrdata/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/ehrdata

Ehrdata is a data framework that comprises a FAIR storage format and a collection of Python libraries for performant access, alignment, and processing of uni- and multi-modal electronic health record datasets.
This repository contains the core ehrdata library.
See the [ehrapy][] package for an analysis package that uses ehrdata to enable the analysis of electronic health record datasetes.

## Getting started

Please refer to the [documentation][],
in particular, the [API documentation][].

## Disclaimer

ehrdata is under heavy construction, and its API not stable.
If you find it potentially interesting for your work, reach out to us via the [scverse zulip platform](https://scverse.zulipchat.com/)!
We can help you using it and will be able to stabilize things you need.

If you have inputs on features, please do not hesitate to open an issue on our [issue tracker][]!

## Installation

You need to have Python 3.11 or newer installed on your system.
If you don't have Python installed, we recommend installing [Mambaforge][].

There are several alternative options to install ehrdata:

1) Install the latest release of `ehrdata` from [PyPI][]:

```bash
pip install ehrdata
```

2. Install the latest development version:

```bash
pip install git+https://github.com/theislab/ehrdata.git@main
```

## Release notes

See the [changelog][].

## Contact

For questions and help requests, you can reach out in the [scverse discourse][].
If you found a bug, please use the [issue tracker][].

## Citation

> t.b.a

[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge
[scverse discourse]: https://discourse.scverse.org
[ehrapy]: https://ehrapy.readthedocs.io/en/stable
[issue tracker]: https://github.com/theislab/ehrdata/issues
[tests]: https://github.com/theislab/ehrdata/actions/workflows/test.yml
[documentation]: https://ehrdata.readthedocs.io
[changelog]: https://ehrdata.readthedocs.io/en/latest/changelog.html
[api documentation]: https://ehrdata.readthedocs.io/en/latest/api.html
[pypi]: https://pypi.org/project/ehrdata

