FunGenKit

FunGenKit is a Python package developed by Gao Wang's Lab, providing a suite of in-house computational tools tailored for functional genomics research. This package focuses on efficient and parallelizable computation methods, including

correlation matrix calculations

Installation

Before installing FunGenKit, ensure you have Python and nbdev installed on your system. FunGenKit is developed using nbdev, which allows for an integrated development process using Jupyter Notebooks.

Install nbdev

If you haven't installed nbdev yet, you can do so using pip:

pip install nbdev

Clone the Repository

Clone the FunGenKit repository to your local machine:

git clone https://github.com/yourusername/FunGenKit.git
cd FunGenKit

Install Dependencies

Make sure all required dependencies are installed:

pip install -r requirements.txt

Usage

FunGenKit is developed in Jupyter Notebooks, where each notebook corresponds to a specific module in the package.

To use the package, simply import it into your Python environment:

from fungenkit import correlation_matrix_in_chunks

Development

To contribute to FunGenKit, follow these steps:

Create a New Notebook: Add a new notebook to the nbs/ folder for additional functionality.
Build the Library: Convert notebooks into Python modules using nbdev_build_lib.
Run Tests: Write and run tests using standard assert statements in your notebooks. Test the entire library with nbdev_test_nbs.
Generate Documentation: Use nbdev_build_docs to create documentation from your notebooks.
Push Changes: Use git to commit and push your changes.

Continuous Integration

FunGenKit uses GitHub Actions for continuous integration. This ensures that all tests pass and the library is correctly built with each push.

Documentation

You can find the complete documentation for FunGenKit at [GitHub Pages URL]. This documentation is automatically generated from the Jupyter Notebooks used to build the library.

Support

If you encounter any problems or have questions, please file an issue on the GitHub repository.

License

FunGenKit is released under the MIT License.

cumc/FunGenKit