Metadata-Version: 2.4
Name: tcia_radiology_processing
Version: 0.1.0
Summary: TCGA Radiogenomics.
Author-email: Joseph Rich <josephrich98@gmail.com>
Maintainer-email: Joseph Rich <josephrich98@gmail.com>
License: BSD 2-Clause License
        
        Copyright (c) 2026, Pachter Lab
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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Project-URL: Homepage, https://github.com/pachterlab/tcia-radiology-processing
Keywords: AI,bioinformatics,deep learning,medicine,radiology
Classifier: Environment :: Console
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: Topic :: Utilities
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: tqdm
Requires-Dist: torchvision
Requires-Dist: pydicom
Requires-Dist: highdicom
Requires-Dist: nibabel
Requires-Dist: scipy
Requires-Dist: simpleitk
Requires-Dist: ipython
Requires-Dist: ipykernel
Requires-Dist: ipywidgets
Requires-Dist: TotalSegmentator
Requires-Dist: dcm2niix
Requires-Dist: pyradiomics
Requires-Dist: openpyxl
Dynamic: license-file

# TCIA Radiogenomics Processing Protocol

Radiology image processing of TCGA/TCIA data.

![alt text](https://github.com/pachterlab/tcia-radiology-processing/blob/main/figures/Fig1.png?raw=true)

## Getting Started

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

```sh
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:

```sh
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:

```sh
pip install -e .
```

## Notebooks
See the [notebooks](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](LICENSE) file for details.

---

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