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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

Usage Demo


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.