https://github.com/saherpathan/bioinnovate
Gene expression analysis and classification using XGBoost and Differential Expression Analysis (DES)
https://github.com/saherpathan/bioinnovate
gene-expression-analysis jupyter-notebook model-training-and-evaluation python3 xgboost-classifier
Last synced: 8 months ago
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Gene expression analysis and classification using XGBoost and Differential Expression Analysis (DES)
- Host: GitHub
- URL: https://github.com/saherpathan/bioinnovate
- Owner: Saherpathan
- License: mit
- Created: 2024-01-21T04:16:57.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-08-15T20:59:48.000Z (about 1 year ago)
- Last Synced: 2025-01-20T04:35:36.980Z (9 months ago)
- Topics: gene-expression-analysis, jupyter-notebook, model-training-and-evaluation, python3, xgboost-classifier
- Language: Jupyter Notebook
- Homepage:
- Size: 2.79 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
BIOINNOVATE
Gene expression analysis and classification using XGBoost and Differential Expression Analysis (DES)
Developed with Jupyter Notebook.
## 🔗 Quick Links
> - [📍 Overview](#-overview)
> - [📦 Features](#-features)
> - [📂 Repository Structure](#-repository-structure)
> - [🚀 Getting Started](#-getting-started)
> - [⚙️ Installation](#️-installation)
> - [🤖 Running Bioinnovate](#-running-bioinnovate)
> - [🤝 Contributing](#-contributing)
> - [📄 License](#-license)
> - [👏 Acknowledgments](#-acknowledgments)
---
## 📍 Overview
BioInnovate performs gene expression analysis and classification using XGBoost. It includes Differential Expression Analysis (DES) to identify significant gene changes and evaluate model performance.
---
## 📦 Features
XGBoost Classification: Utilizes XGBoost for gene expression classification
Differential Expression Analysis (DES): Identifies differentially expressed genes
Visualization: Includes feature importance and correlation heatmaps
---
## 📂 Repository Structure
```sh
└── BioInnovate/
├── GSE250323.csv
├── README.md
├── Visuals.ipynb
└── Modeling.ipynb
```
---
## 🧩 Files
.
| File | Summary |
| --- | --- |
| [Visuals.ipynb](https://github.com/Saherpathan/BioInnovate/blob/master/Visuals.ipynb) | Implements Differential Expression Analysis and visualizations |
| [Modeling.ipynb](https://github.com/Saherpathan/BioInnovate/blob/master/iitj_bioinnovate.ipynb) | Trains and evaluates XGBoost classifier, analyzes feature importance |
---
## 🚀 Getting Started
***Requirements***
Ensure you have the following dependencies installed on your system:
* **JupyterNotebook**: `version v6`
### ⚙️ Installation
1. Clone the BioInnovate repository:
```sh
git clone https://github.com/Saherpathan/BioInnovate
```
2. Change to the project directory:
```sh
cd BioInnovate
```
3. Install the dependencies:
```sh
pip install -r requirements.txt
```
### 🤖 Running BioInnovate
Use the following command to run BioInnovate:
```sh
jupyter nbconvert --execute Visuals.ipynb
jupyter nbconvert --execute Modeling.ipynb
```
---
## 🤝 Contributing
Contributions are welcome! Here are several ways you can contribute:
- **[Submit Pull Requests](https://github.com/Saherpathan/BioInnovate/blob/main/CONTRIBUTING.md)**: Review open PRs, and submit your own PRs.
- **[Join the Discussions](https://github.com/Saherpathan/BioInnovate/discussions)**: Share your insights, provide feedback, or ask questions.
- **[Report Issues](https://github.com/Saherpathan/BioInnovate/issues)**: Submit bugs found or log feature requests for Bioinnovate.
Contributing Guidelines
1. **Fork the Repository**: Start by forking the project repository to your GitHub account.
2. **Clone Locally**: Clone the forked repository to your local machine using a Git client.
```sh
git clone https://github.com/Saherpathan/BioInnovate
```
3. **Create a New Branch**: Always work on a new branch, giving it a descriptive name.
```sh
git checkout -b new-feature-x
```
4. **Make Your Changes**: Develop and test your changes locally.
5. **Commit Your Changes**: Commit with a clear message describing your updates.
```sh
git commit -m 'Implemented new feature x.'
```
6. **Push to GitHub**: Push the changes to your forked repository.
```sh
git push origin new-feature-x
```
7. **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.
---
## 📄 License
This project is protected under the MIT License.
---
## 👏 Acknowledgments
- Data: Gene expression data from GSE250323.
- Libraries: XGBoost, Jupyter Notebook, and Seaborn for analysis and visualization.
---
## 👥 Contributors
- **Saher Pathan** - [GitHub Profile](https://github.com/Saherpathan)
- **Khushi Mohurle** - [GitHub Profile]()
- **Sayali Warkade** - [GitHub Profile]()
[**Return**](#-quick-links)
---