Hi! We are Anika, Tara, and Erik, 3 biomedical engineering seniors at USC. This repository is our senior design project: an automated sc-RNA sequencing web application designed for researchers who have no coding experience. Please feel free to contact us at anikagup@usc.edu (Anika), taranate@usc.edu (Tara), and noyman@usc.edu (Erik), with any questions, comments, or concerns!
- Download the Docker Desktop from here: https://www.docker.com/products/docker-desktop/
- Install Git here from: https://git-scm.com/downloads
- Clone the Github repository in the local computer’s terminal/command prompt by running each command once, separately: git clone https://github.com/anikagup/scRNA-seq-Automation.git cd scRNA-seq-Automation
- Start the app by running: docker-compose up --build
- Paste this link in your browser to run the app: http://localhost:8000
- Upload a supported .h5ad, .csv, .h5, .loom, or .fastq file.
- Click Run Analysis to start preprocessing and visualization.
- Adjust QC parameters and click Reprocess to regenerate figures.
- Enter a gene you know is in your dataset and click Generate UMAP to view expression patterns.
- Download the Processed CSV or DEG List using the provided buttons.
- To stop the app when you are done, first Press Ctrl C, then run docker-compose down
Important notes:
- Check that no virtual environment (venv) of any kind is running, you want to see the name of your computer as the first thing in the terminal
- docker-compose build --no-cache # build and save space
- docker-compose up -d # to run app after build
- If met with errors, paste "docker-compose logs frontend" into terminal and evaluate output