The Patient Data Expander Tool allows researchers to identify clusters within their patient data sets, select the features that best define those clusters, then query public databases for similar patients and export their data to expand their initial dataset.
Project description
Usage
Installation
You can install the Patient Data Expander Tool directly from PyPI using pip:
pip install patient-data-expander-tool
How to run
Once installed, you can run from your terminal by running:
run_pdet
Input data tips
For the expander tool to analyse your patient data most effectively:
- Ensure your uploaded CSV file includes columns with full named headers rather than abbreviations (you can change these within the app too).
- Do not include derived columns i.e. "Colorectal Cancer" [Yes/No] derived from "Cancer Type" [Breast, Colorectal, Testicular...etc] as these will be unlikely to match to public databases.
- Ensure data is as complete as possible. There is a removal/imputation stage within the tool, but the more complete your data is, the better.
Acknowledgements
Tool created by Joseph Cottrell under the supervision of Ferran Cardoso at the Integrated Pathology Unit.
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