Source cords for "AMC bladder cancer protein digger"

This repository contains code for identifying potential immunohistochemistry (IHC) markers that predict patient responses (either non-response (NR) or response (R)) to neoadjuvant chemotherapy in bladder cancer, based on transcriptomics data from the AMC (Asan Medical Center) datasets. The pipeline is implemented in Python (version 3.12).

Clone the repository and create necessary directories for the project:

git clone https://github.com/JinahnJ/amc-BC-protein-digger
cd amc-sdm-ml-bc
md dst
md src

Create and activate the environment using Poetry:

poetry shell

Before running the code, check and configure the settings file in the ./config directory.

To classify patient responses, use:

Before running the code, ensure you have checked and properly edited the configuration file, typically located in the ./config directory.

You can run the classifier using:

python main.py -c CONFIG-PATH -r RESULT-PATH

Alternatively, you can use the provided shell script:

./run.sh

The output will be saved by default in ./src/results.yaml.

• The dataset is available upon request by contacting the corresponding author of the following paper: https://doi.org/10.1016/j.xcrm.2023.101224