RNA Explorer (RNA-E) is an Amazon Web Services (AWS) hosted web application, designed for quick and easy analysis of raw bulk RNA sequencing (RNA-seq) data. Users can upload a CSV file containing raw gene expression counts data and RNA-E will quickly produce useful detailed tables and visualizations. As RNA-E is hosted on AWS, RNA-E is scalable, secure and efficient and, in its current state, can handle 10-20 concurrent users.
- CSV File Upload: Upload raw bulk RNA-seq data in CSV format (samples as columns, genes as rows).
- Data Table: View processed gene expression data in easy to use tables.
- Data Visualization: View nice and clear graphs to explore gene expression.
- AWS Integration: RNA-E leverages AWS for data storage, computation, and deployment to provide a robust and scalable web-app solution for on-the-go bioinformatics. This web-app
- CI/CD RNA_E has CI/CD implemented, meaning pushes to main are deployed on AWS.
- User Authentication: RNA-E has integrity - with a secure login system to protect data and maintain privacy.
- Frontend: Bootstrap CSS framework (https://getbootstrap.com/) and DataTables Javascript HTML table library (https://datatables.net/).
- Backend: Python 3.9 Flask 3.0.3 web framework.
- Data Processing: Pandas 2.2.2 and numpy 2.0.1 for data manipulation and matplotlib 3.9.2 and Seaborn 0.13.2 for plotting.
- Deployment: AWS for application deployment, Flask-SQLAlchemy 3.1.1 SQLite based Flask-login 0.6.3 for authentication, CloudWatch for monitoring.
- Version Control: Git, hosted on GitHub with CI/CD implemented via GitHub Actions.
- Clone the repository:
git clone https://github.com/YEBADI/rna_explorer.git
cd rna_explorer
- Set up the environment:
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
- Run the application:
python app/app.py
This project is licensed under the MIT License - see the LICENSE file for details.
For any inquiries or support, please contact yusefbadi@gmail.com.