This website is hosted at: https://sib-swiss.github.io/seq-spatial-transcriptomics-training

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

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

Course website biology-informed-multiomics

Authors

• Deepak Tanwar ORCiD
• Joana Carlevaro-Fita ORCiD
• Geert van Geest ORCiD
• Julien Roux ORCiD
• Martin Emons ORCiD
• Peiying Cai ORCiD
• Ivan Berest ORCiD
• Mark Robinson ORCiD

Local Development

This website is generated with quarto. To contribute or run the material locally, you will need to have R and Quarto CLI installed.

1. Clone the repository:

   git clone https://github.com/sib-swiss/seq-spatial-transcriptomics-training.git
   cd seq-spatial-transcriptomics-training

2. Install R packages: This project uses renv to manage R dependencies. To install the required packages, open R and run:

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

3. Render the site: To build the website, run the following command in the terminal:

   quarto render

   This will generate the website in the _site directory.

4. Preview the site: To preview the website as you make changes, you can use:

   quarto preview

Publishing

To publish the website to GitHub Pages, use the following command:

quarto publish gh-pages

This will render the site and push the _site directory to the gh-pages branch. Make sure you have the necessary permissions to push to the repository.

Docker

For a reproducible environment, you can use the provided Docker setup. A pre-built Docker image is available on Docker Hub.

1. Pull the Docker image:

   docker pull sibswiss/training-seq-spatial-transcriptomics-rstudio:latest

2. Run the Docker container: Navigate to the Docker directory and use the provided script to run the container:

   cd Docker
   ./run_locally.sh

   Alternatively, you can run the container manually from the project root directory:

   docker run --rm -p 8787:8787 -v $PWD:/home/rstudio sibswiss/training-seq-spatial-transcriptomics-rstudio:latest

   This will start an RStudio server on http://localhost:8787. The -v $PWD:/home/rstudio command mounts the current directory into the container, so you can edit the files locally and see the changes reflected in the container.