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TCIA Radiogenomics Processing Protocol

Radiology image processing of TCGA/TCIA data.

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Getting Started

To run the code in this repository, follow these steps:

git clone https://github.com/pachterlab/tcia-radiology-processing.git
cd tcia-radiology-processing

We recommend using an environment manager such as conda. Some additional non-python packages must be installed for full functionality. If using conda (recommended), simply run the following:

conda env create -f environment.yml
conda activate tcia_radiology_processing

Otherwise, install these packages manually as-needed (see environment.yml and pyproject.toml for the list of packages and recommended versions).

(Optional) For development, explicitely install the package in editable mode with the following command:

pip install -e .

Notebooks

See the notebooks directory for the data processing protocol in a Jupyter notebook format.

License

This project is licensed under the BSD 2-Clause License. See the LICENSE file for details.

For any issues or contributions, feel free to open a pull request or issue in this repository.