About This Repository

Hi! We are Anika, Tara, and Erik, 3 biomedical engineering seniors at USC. This is a template repository, meaning you can make your own repository containing all of these files and the structure we have left for you! 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!

To Run App Through Docker

1. Download the Docker Desktop from here: https://www.docker.com/products/docker-desktop/
2. Install Git here from: https://git-scm.com/downloads
3. 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
4. Start the app by running: docker-compose up --build
5. Paste this link in your browser to run the app: http://localhost:8000
6. Upload a supported .h5ad, .csv, .h5, .loom, or .fastq file.
7. Click Run Analysis to start preprocessing and visualization.
8. Adjust QC parameters and click Reprocess to regenerate figures.
9. Enter a gene you know is in your dataset and click Generate UMAP to view expression patterns.
10. Download the Processed CSV or DEG List using the provided buttons.
11. To stop the app when you are done, first Press Ctrl C, then run docker-compose down

Important notes:

1. 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
2. docker-compose build --no-cache # build and save space
3. docker-compose up -d # to run app after build
4. If met with errors, paste "docker-compose logs frontend" into terminal and evaluate output

scRNA-seq-Automation

pip install -r requirements.txt

python src/main.py

shiny run UI/app.py

docker-compose build --no-cache after this, you need to run "docker-compose up -d" to actually start the docker and when leaving VSCode, run "docker-compose down" # To run in background

git add # After resolving git commit -m "" # Finish merge git push origin main # Push if needed

git status # to see what files you have made changes to

Not needed anymore

for xg boost, libomp: first,

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" # takes about five mins

add to path (for M chip mac)

echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> ~/.zprofile eval "$(/opt/homebrew/bin/brew shellenv)"

then

brew install libomp