Metadata-Version: 2.4
Name: pdet
Version: 0.1.0
Summary: 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.
Requires-Python: >=3.13
Description-Content-Type: text/markdown
Requires-Dist: ehrapy>=0.14.0
Requires-Dist: ehrdata>=0.2.1
Requires-Dist: holoviews>=1.22.1
Requires-Dist: hvplot>=0.12.2
Requires-Dist: ipykernel>=7.3.0
Requires-Dist: matplotlib>=3.11.0
Requires-Dist: nbdev>=3.0.17
Requires-Dist: pandas>=3.0.3
Requires-Dist: panel>=1.9.3
Requires-Dist: rapidfuzz>=3.14.5
Requires-Dist: scikit-learn>=1.9.0
Requires-Dist: sentence-transformers>=5.5.1
Requires-Dist: wordninja>=2.0.0

![PyPI - Version](https://img.shields.io/pypi/v/patient-data-expander-tool)

# Usage

## Installation

You can install the **Patient Data Expander Tool** directly from PyPI using `pip`:

```bash
pip install patient-data-expander-tool
```

## How to run

Once installed, you can run from your terminal by running:

```bash
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](https://github.com/Jobot99) under the supervision of [Ferran Cardoso](https://github.com/fercrcode) at the Integrated Pathology Unit.
