https://github.com/theislab/ehrapy

Electronic Health Record Analysis with Python.
https://github.com/theislab/ehrapy

ehr electronic-health-record electronic-medical-record scverse

Last synced: 8 months ago
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Electronic Health Record Analysis with Python.

• Host: GitHub
• URL: https://github.com/theislab/ehrapy
• Owner: theislab
• License: apache-2.0
• Created: 2021-06-11T13:01:50.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2025-10-07T13:43:13.000Z (8 months ago)
• Last Synced: 2025-10-07T15:31:49.410Z (8 months ago)
• Topics: ehr, electronic-health-record, electronic-medical-record, scverse
• Language: Python
• Homepage: https://ehrapy.readthedocs.io/
• Size: 188 MB
• Stars: 308
• Watchers: 3
• Forks: 36
• Open Issues: 37
• Metadata Files:
  • Readme: README.md
  • Contributing: docs/contributing.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

          
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# ehrapy overview

**ehrapy** is a modular open-source Python framework for exploratory analysis of heterogeneous epidemiological and EHR data.

It supports a full pipeline from data ingestion and quality control to advanced analyses such as clustering, survival, trajectory, causal inference, deep learning, and more.



  



## Documentation

Please read the [documentation](https://ehrapy.readthedocs.io/en/latest) for installation, tutorials, use cases, and more.

## Installation

You can install _ehrapy_ via [pip] from [PyPI]:

```console

$ pip install ehrapy

```

## API

Please have a look at the [API documentation](https://ehrapy.readthedocs.io/en/latest/api.html) and the [tutorials](https://ehrapy.readthedocs.io/en/latest/tutorials/index.html).

```python

import ehrapy as ep

```

## Citation

 


  

    

  



Read more about ehrapy in the [associated publication](https://doi.org/10.1038/s41591-024-03214-0).

```bibtex

@article{Heumos2024,

  author = {Heumos, Lukas and Ehmele, Philipp and Treis, Tim and Upmeier zu Belzen, Julius and Roellin, Eljas and May, Lilly and Namsaraeva, Altana and Horlava, Nastassya and Shitov, Vladimir A. and Zhang, Xinyue and Zappia, Luke and Knoll, Rainer and Lang, Niklas J. and Hetzel, Leon and Virshup, Isaac and Sikkema, Lisa and Curion, Fabiola and Eils, Roland and Schiller, Herbert B. and Hilgendorff, Anne and Theis, Fabian J.},

  year = {2024},

  month = {11},

  day = {01},

  title = {An open-source framework for end-to-end analysis of electronic health record data},

  journal = {Nature Medicine},

  volume = {30},

  number = {11},

  pages = {3369--3380},

  issn = {1546-170X},

  doi = {10.1038/s41591-024-03214-0},

  url = {https://doi.org/10.1038/s41591-024-03214-0}

}

```

[pip]: https://pip.pypa.io/

[pypi]: https://pypi.org/

[api]: https://ehrapy.readthedocs.io/en/latest/api.html