Precourse

RaukR 2025 • R Beyond the Basics

Preparation and system set-up for the workshop

1 Location

Campus Gotland
Uppsala University
Cramérgatan 3
621 57 Visby
Gotland, Sweden

We will use classrooms B25 and B27 on Floor 2 (on map) throughout the workshop. We may use other rooms for Online sessions. Lunches and coffee/tea will be served in the Cafe next to it on the ground floor.

Tip

If you have a door access card for Uppsala university, take it with you.

2 Computer

You can use any system you like, but we recommend using a Linux or Mac system. It’s good to have about 20GB of free space on your system. If you are using Windows, we recommend using WSL2 (Windows Subsystem for Linux). This will allow you to run a Linux environment on your Windows machine.

Warning

Make sure you have administrative rights on your system. You will need to install software and packages. Make sure you set-up Eduroam for wifi at your home institution before you leave.

3 Software

You will need the following list of software tools and a list of R packages for the Hands-on practical labs.

  • R 4.4
  • IDE (Latest RStudio, Positron or VS Code)
  • Quarto 1.5.57 or newer
  • Conda (Miniforge recommended)
  • Slack (https://raukr.slack.com/) Invitation will be sent to your email
  • Git
  • Browser (Chrome, Firefox, Safari etc)
  • Docker (Optional)

3.1 Conda

Install Miniforge. Test that it works and then create a new environment and activate it.

Terminal
conda create -n raukr -c conda-forge -c bioconda r-base=4.4 r-tidyverse r-essentials r-svglite quarto freetype libpng libxml2 pkg-config zlib xz bioconda::htslib gdal proj
conda activate raukr

To install packages, see installation instructions below. If you are using the docker container, you don’t need Conda.

4 R packages

You can save valuable time during the labs by setting up the environment and installing the R packages in advance. You can choose between two options:

  • Manual installation
  • Using docker container

4.1 Manual installation

You assume full responsibility for setting up your environment. This means you will need to install R, RStudio and R packages on your own. You can have a local installation but we suggest that you work in a Conda environment. Here is the list of R packages you will need to install:

Install CRAN packages if they are not already installed.

pkgs_cran <- c('BiocManager', 'bsplus', 'devtools', 'dplyr', 'DT', 'eulerr', 'fontawesome', 'ggiraph', 'ggplot2', 'ggrepel', 'gitcreds', 'googledrive', 'gt', 'here', 'htmltools', 'hues', 'jsonlite', 'kableExtra', 'keras', 'knitr', 'lubridate', 'magrittr', 'MASS', 'microbenchmark', 'optparse', 'patchwork', 'peakRAM', 'plotly', 'profr', 'proftools', 'profvis', 'pryr', 'purrr', 'R.utils', 'R6', 'readr', 'readxl', 'remotes', 'renv', 'reticulate', 'rlang', 'rmarkdown', 'roxygen2', 'rpart', 'rpart.plot', 'shiny', 'sm', 'spatstat', 'stringr', 'tibble', 'tictoc', 'tidyr', 'tidyverse', 'usethis')

for( pkg in pkgs_cran) {
  if (!requireNamespace(pkg, quietly = TRUE)) {
    install.packages(pkg, repos = 'https://packagemanager.rstudio.com/all/latest', verbose = TRUE)
  }
}

Install Bioconductor packages.

BiocManager::install(c('Rgraphviz','RNASeqPower','ShortRead'), update = TRUE, ask = FALSE)

Install GitHub packages.

remotes::install_github(repo = 'rstudio/EDAWR', ref = 'fbfee98447826f6b199a482715f3b7dadd311da3', host = 'api.github.com')
remotes::install_github(repo = 'hadley/emo', ref = '3f03b11491ce3d6fc5601e210927eff73bf8e350', host = 'api.github.com')

4.2 Using docker container

We provide a docker container with all the required packages pre-installed. This is the easiest way to set up your environment, as you don’t need an R or RStudio installation on your local machine. But you will need to have docker installed. Follow the instructions on DockerDocs to install docker on your system.

Once you have verified that it works, run the following command in the terminal.

Terminal
docker run --platform=linux/amd64 -e PASSWORD=raukr -p 8787:8787 -p 4200:4200 -v ${PWD}:/home/rstudio/work ghcr.io/nbisweden/workshop-raukr:latest

This will launch an instance of RStudio Server. In the browser, go to http://localhost:8787/. Use following credentials:

username: rstudio
password: raukr

5 Course materials

Course materials will be made available on https://nbisweden.github.io/raukr-2025/home_contents.html once the workshop begins. You can copy-paste code from the website to your R session.

Alternatively, you can also download/clone the materials from GitHub and run them locally. To do this, go to https://github.com/NBISweden/raukr-2025 and click on the green Code button. You can either download the materials as a zip file (Download ZIP) or clone the repository using git. If you are using git, run the following command in your terminal:

Terminal
git clone https://github.com/NBISweden/raukr-2025.git

This will create a folder called raukr-2025 in your current working directory. You can then open the materials in RStudio or any other IDE of your choice. Or run a docker container as previous described.

The course materials on GitHub and the website will persist after the workshop. You can use them as a reference in the future.