flask-scrna-spermatogenesis

flask-scrna-spermatogenesis is a web application designed to visualize single-cell RNA sequencing (scRNA-seq) datasets, specifically focusing on gene expression during spermatogenesis.

Features

• Upload your own gene list from a file
• Enter gene names directly
• Visualize gene expression dynamics across different stages of spermatogenesis

Set up locally

Follow these steps to run the app locally.

1. Create a virtual environment:

   python3 -m venv venv
   source venv/bin/activate

2. Upgrade pip and install necessary packages:

   python3 -m pip install --upgrade pip
   pip install flask pandas matplotlib seaborn scipy

3. Run the app:

   # python app.py

4. If you are running on a CentOS server, you might need to allow traffic on port 5000:

   sudo firewall-cmd --zone=public --add-port=5000/tcp --permanent
   sudo firewall-cmd --reload

5. Set the FLASK_APP environment variable and start the server:

   export FLASK_APP=${HOME}/src/flask-scrna-spermatogenesis/app.py
   flask run --host=0.0.0.0 --port=5000

6. Open your web browser and navigate to http://localhost:5000

License

This project is licensed under the terms of the MIT license.

Source Code

The source code for this project is available on GitHub.