Usage

Install

1. Install uv:

• Open terminal -- Windows Powershell: powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" -- WLS/macOS/Linux shell: curl -LsSf https://astral.sh/uv/install.sh | sh
• Close and open a new terminal

2. Clone/download repo from https://github.com/Jobot99/Patient-Data-Expander-Tool

3. Open terminal, navigate to the Patient Data Expander Tool directory and run

uv sync

to install necessary packages.

Run

To run pdet use

uv run python -m 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.
• Ensure that patient id column is named one of the following: "cprid", "patient_id", "patientid", "id", "subject_id".

Acknowledgements

Tool created by Joseph Cottrell under the supervision of Ferran Cardoso at the Integrated Pathology Unit.