https://github.com/bhklab/ispy-readii
Running READII on the I-SPY cohort for radiogenomic analysis.
https://github.com/bhklab/ispy-readii
Last synced: 3 months ago
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Running READII on the I-SPY cohort for radiogenomic analysis.
- Host: GitHub
- URL: https://github.com/bhklab/ispy-readii
- Owner: bhklab
- License: mit
- Created: 2024-11-13T16:47:46.000Z (7 months ago)
- Default Branch: main
- Last Pushed: 2025-03-22T03:03:15.000Z (3 months ago)
- Last Synced: 2025-03-22T03:19:34.661Z (3 months ago)
- Language: Python
- Size: 122 MB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ispy-readii
Running READII to perform radiomic feature extraction on the I-SPY cohort for radiogenomic analysis.
## Development
### Installing Pixi
Pixi is a tool for managing conda environments and managing dependencies.
To install pixi, visit the [pixi website](https://pixi.sh/) and follow the instructions for your operating system.
### Cloning the repository
Clone the repository to your local machine using the following command:
```bash
git clone https://github.com/bhklab/RECIST-play.git
```
### Installing dependencies
To install the dependencies for the handbook, run the following command:
```bash
pixi install
```
This will install the dependencies specified in the `pixi.toml` file.
### Adding dependencies
To add a new dependency, run the following command:
```bash
pixi add
```
This will add the specified package to the `pixi.toml` file.
## Directory Structure
Run the following command in your terminal in the ispy-readii directory to set up the project directory structure:
```shell
mkdir -p procdata rawdata results workflow/{config,envs,logs,notebooks,scripts}
```
You should now have the following directory structure:
```bash
├── README.md
├── procdata # output from any processing steps of rawdata
├── rawdata # data as it is downloaded from the source
├── results # final output from the pipeline
└── workflow
├── config
├── envs
├── logs
├── notebooks # Jupyter, R notebooks
└── scripts # Where any code scripts are kept (Python, R, etc.)
```
## Contributing
Please use the following angular commit message format:
```
(optional scope): short summary in present tense
(optional body: explains motivation for the change)
(optional footer: note BREAKING CHANGES here, and issues to be closed)
```
`` refers to the kind of change made and is usually one of:
- `feat`: A new feature.
- `fix`: A bug fix.
- `docs`: Documentation changes.
- `style`: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc).
- `refactor`: A code change that neither fixes a bug nor adds a feature.
- `perf`: A code change that improves performance.
- `test`: Changes to the test framework.
- `build`: Changes to the build process or tools.
`scope` is an optional keyword that provides context for where the change was made. It can be anything relevant to your package or development workflow (e.g., it could be the module or function - name affected by the change).