INR-Gate

Python reference code for the Informative-Negative Rechallenge Gate (INR-Gate), a statistical simulation framework for interpreting a plasma ctDNA result with no covered anti-EGFR resistance SNV/indel detected in metastatic colorectal cancer.

Important scope

This repository contains deterministic synthetic data only. It does not contain patient-level CHRONOS data, estimate treatment benefit, make treatment recommendations, or establish clinical validation. The implementation supports only SNV/indel mutant-molecule observations; CNVs, amplifications, fusions, structural variants, MSI, methylation, expression, and raw-read-depth proxies are outside its certificate scope.

Run the synthetic demonstration

Python 3.11 or newer is required.

python -m venv .venv
# Windows: .venv\\Scripts\\activate
# macOS/Linux: source .venv/bin/activate
python -m pip install -e .
python -m pip install -r requirements.txt
python -m unittest discover -s tests -v
python -m inrg synthetic-demo --config configs/synthetic_demo.toml --output-dir synthetic_run

To regenerate the four composite simulation figures, run:

python -m inrg figures --config configs/synthetic_demo.toml --output-dir figure_run