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<img src="https://user-images.githubusercontent.com/21954664/156930990-0d668468-0cd9-496e-995a-96d2c2407cf5.png" alt="ehrapy logo">





  
  

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ehrapy is a modular open-source Python framework designed for exploratory end-to-end analysis of heterogeneous epidemiology and electronic health record data.





  
  

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```{eval-rst}





  
  

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.. card:: Installation :octicon:`plug;1em;`





  
  

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    :link: installation





  
  

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    :link-type: doc





  
  

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    New to *ehrapy*? Check out the installation guide.





  
  

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```





  
  

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```{eval-rst}





  
  

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.. card:: API reference :octicon:`book;1em;`





  
  

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    :link: usage/usage





  
  

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    :link-type: doc





  
  

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    The API reference contains a detailed description of the ehrapy API.





  
  

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```





  
  

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```{eval-rst}





  
  

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.. card:: Tutorials :octicon:`play;1em;`





  
  

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    :link: tutorials/index





  
  

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    :link-type: doc





  
  

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    The tutorials walk you through real-world applications of ehrapy.





  
  

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```





  
  

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```{eval-rst}





  
  

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.. card:: Discussion :octicon:`megaphone;1em;`





  
  

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    :link: https://discourse.scverse.org/





  
  

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    Need help? Reach out on our forum to get your questions answered!





  
  

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```





  
  

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```{eval-rst}





  
  

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.. card:: GitHub :octicon:`mark-github;1em;`





  
  

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    :link: https://github.com/theislab/ehrapy





  
  

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    Find a bug? Interested in improving ehrapy? Checkout our GitHub for the latest developments.





  
  

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```





  
  

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```{toctree}





  
  

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:caption: 'Contents:'





  
  

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:hidden: true





  
  

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:maxdepth: 3





  
  

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installation





  
  

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usage/usage





  
  

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tutorials/index





  
  

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contributing





  
  

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references





  
  

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```





  
  

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# Citation





  
  

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[Exploratory electronic health record analysis with ehrapy Lukas Heumos, Philipp Ehmele, Tim Treis, Julius Upmeier zu Belzen, Altana Namsaraeva, Nastassya Horlava, Vladimir A. Shitov, Xinyue Zhang, Luke Zappia, Rainer Knoll, Niklas J. Lang, Leon Hetzel, Isaac Virshup, Lisa Sikkema, Eljas Roellin, Fabiola Curion, Roland Eils, Herbert B. Schiller, Anne Hilgendorff, Fabian J. Theis





  
  

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medRxiv 2023.12.11.23299816; doi: https://doi.org/10.1101/2023.12.11.23299816 ](https://www.medrxiv.org/content/10.1101/2023.12.11.23299816v1).





  
  

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# Indices and tables





  
  

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- {ref}`genindex`





  
  

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- {ref}`modindex`





  
  

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- {ref}`search`





  
  

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[scanpy genome biology (2018)]: https://doi.org/10.1186/s13059-017-1382-0