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eds-scikit is a tool to assist data scientists working on the AP-HP's Clinical Data Warehouse. It is specifically targeted for OMOP-standardized data. It main goals are to: - Ease access and analysis of data - Allow a better transfer of knowledge between projects - Improve research reproducibility ## Development This library is developed and maintained by the core team of AP-HP’s Clinical Data Warehouse (EDS) with the strong support of [Inria's SODA team](https://team.inria.fr/soda/). ## How to use Please check the [online documentation](https://aphp.github.io/eds-scikit/) for more informations. You will find - Detailed explanation of the project goal and working principles - A complete API documentation - Various Jupyter Notebooks describing how to use various functionnalities of eds-scikit - And more ! ## Requirements eds-scikit stands on the shoulders of [Spark 2.4](https://spark.apache.org/docs/2.4.8/index.html) which requires: - Python ~3.7.1 - Java 8 ## Installation You can install eds-scikit via `pip`: ```bash pip install "eds-scikit[aphp]" ``` :warning: If you get an an error during installation, please try downgrading pip via `pip install -U "pip<23" before install `eds-scikit` :warning: If you don't work in AP-HP's ecosystem (EDS), please install via: ```bash pip install eds-scikit ``` You can now import the library via ```python import eds_scikit ``` ### Contributing - You want to help on the project ? - You developped an interesting feature and you think it could benefit other by being integrated in the library ? - You found a bug ? - You have a question about the library ? - ... Please check our [contributing guidelines](https://aphp.github.io/eds-scikit/contributing/). ### Citation If you use `eds-scikit`, please cite us as below. ```bibtex @misc{eds-scikit, author = {Petit-Jean, Thomas and Remaki, Adam and Maladière, Vincent and Varoquaux, Gaël and Bey, Romain}, doi = {10.5281/zenodo.7401549}, title = {eds-scikit: data analysis on OMOP databases}, url = {https://github.com/aphp/eds-scikit} } ``` ### Acknowledgment We would like to thank the following funders: - [Assistance Publique – Hôpitaux de Paris](https://www.aphp.fr/) - [AP-HP Foundation](https://fondationrechercheaphp.fr/) - [Inria](https://www.inria.fr)