This website is hosted at: https://sib-swiss.github.io/single-cell-training/

Please refer to issues for improvements/bugs for course material or the website.

Any contribution to this course material is highly appreciated :+1:. Please have a look at the CONTRIBUTING.md file to learn more on how to contribute.

Course website single cell transcriptomics

Authors

• Tania Wyss ORCiD
• Rachel Marcone-Jeitziner ORCiD
• Geert van Geest ORCiD
• Patricia Palagi ORCiD

How reuse this material

This website is generated with quarto. To re-build the website, download and install Rstudio and Quarto CLI. Also make sure you have installed the required packages. After that, clone this repository:

git clone https://github.com/sib-swiss/single-cell-r-training.git

Using renv

This project uses renv to manage R dependencies. To restore the project's environment, run the following commands in R:

install.packages("renv")
renv::restore()

Render website

Open the project in Rstudio, and run in the terminal to render the full website:

quarto render

Or to preview the website:

quarto preview

To publish the website to GitHub Pages, run:

quarto publish gh-pages

Run with Docker

A Docker image with all the required software is available on Docker Hub.

To run the Docker container, you can use the following command:

docker run \
--rm \
-p 8787:8787 \
-v $PWD:/home/rstudio \
sibswiss/training-singlecell-rstudio:latest

You can also use the script Docker/run_locally.sh to run the container.

Update Docker image

To add or update R packages in the Docker image, you need to:

1. Add the new packages to the Docker/install_packages.R script.
2. Copy the renv.lock file from the root directory to the Docker directory.
3. Rebuild the Docker image.

Using GitHub Actions

You can manually trigger a build of the Docker image by going to the Actions tab of this repository, selecting the "Manual build and push" workflow, and clicking "Run workflow".

Locally

Alternatively, you can rebuild the image locally:

cp renv.lock Docker/
cd Docker
docker build -t sibswiss/training-singlecell-rstudio:latest .