Gene expression analysis and classification using XGBoost and Differential Expression Analysis (DES)
Developed with Jupyter Notebook.
BioInnovate performs gene expression analysis and classification using XGBoost. It includes Differential Expression Analysis (DES) to identify significant gene changes and evaluate model performance.
XGBoost Classification: Utilizes XGBoost for gene expression classification
Differential Expression Analysis (DES): Identifies differentially expressed genes
Visualization: Includes feature importance and correlation heatmaps
└── BioInnovate/
├── GSE250323.csv
├── README.md
├── Visuals.ipynb
└── Modeling.ipynb.
| File | Summary |
|---|---|
| Visuals.ipynb | Implements Differential Expression Analysis and visualizations |
| Modeling.ipynb | Trains and evaluates XGBoost classifier, analyzes feature importance |
Requirements
Ensure you have the following dependencies installed on your system:
- JupyterNotebook:
version v6
- Clone the BioInnovate repository:
git clone https://github.com/Saherpathan/BioInnovate- Change to the project directory:
cd BioInnovate- Install the dependencies:
pip install -r requirements.txtUse the following command to run BioInnovate:
jupyter nbconvert --execute Visuals.ipynb
jupyter nbconvert --execute Modeling.ipynbContributions are welcome! Here are several ways you can contribute:
- Submit Pull Requests: Review open PRs, and submit your own PRs.
- Join the Discussions: Share your insights, provide feedback, or ask questions.
- Report Issues: Submit bugs found or log feature requests for Bioinnovate.
Contributing Guidelines
- Fork the Repository: Start by forking the project repository to your GitHub account.
- Clone Locally: Clone the forked repository to your local machine using a Git client.
git clone https://github.com/Saherpathan/BioInnovate
- Create a New Branch: Always work on a new branch, giving it a descriptive name.
git checkout -b new-feature-x
- Make Your Changes: Develop and test your changes locally.
- Commit Your Changes: Commit with a clear message describing your updates.
git commit -m 'Implemented new feature x.' - Push to GitHub: Push the changes to your forked repository.
git push origin new-feature-x
- Submit a Pull Request: Create a PR against the original project repository. Clearly describe the changes and their motivations.
Once your PR is reviewed and approved, it will be merged into the main branch.
This project is protected under the MIT License.
- Data: Gene expression data from GSE250323.
- Libraries: XGBoost, Jupyter Notebook, and Seaborn for analysis and visualization.
- Saher Pathan - GitHub Profile
- Khushi Mohurle - GitHub Profile
- Sayali Warkade - GitHub Profile