Precourse

RaukR 2026 • Data Science With R

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, you will likely need 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 4.5
  • IDE (Latest RStudio, Positron or VS Code)
  • Quarto 1.8.25 or newer
  • Slack (https://raukr.slack.com/) Invitation will be sent to your email
  • Git
  • Browser (Chrome, Firefox, Safari etc)
  • Conda (Optional, Miniforge recommended)
  • Docker (Optional)

It’s better to install R and install necessary packages in an isolated environment for the workshop rather than installing directly onto the system. That way, it’s also convenient to remove everything after the workshop. You can use a Conda environment, pixi environment or a docker container.

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=4.5 r-tidyverse r-essentials r-svglite r-ragg r-systemfonts quarto freetype libpng libxml2 pkg-config zlib xz bioconda::htslib gdal proj libzmq3-dev
conda activate raukr

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

3.2 Pixi

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

Terminal
pixi init --channel conda-forge --channel bioconda raukr
cd raukr
pixi add r-base=4.5 r-tidyverse r-essentials r-svglite r-ragg r-systemfonts quarto freetype libpng libxml2 pkg-config zlib xz htslib gdal proj
pixi shell

4 R packages

You can install R packages for each lab as you go. Alternatively, you can save some time during the labs by setting up the environment and installing the R packages in advance. You can use either use renv or manually install.

4.1 Renv

Create a work directory and download the lockfile into it.

renv.lock

Then, restore packages from the lockfile.

install.packages(c("renv", "pak", "gitcreds"))
options(renv.config.pak.enabled = TRUE)
renv::init()

Select ‘1: Restore the project from the lockfile.’

Based on missing system libraries, you may need to install additional system dependencies and re-run installation.

4.2 Manual

Here is the list of R packages you will need to install:

Install CRAN packages if they are not already installed.

pkgs_cran <- c('bench', 'bsplus', 'data.table', 'devtools', 'dplyr', 'DT', 'eulerr', 'fontawesome', 'ggiraph', 'ggplot2', 'ggrepel', 'gt', 'here', 'htmltools', 'hues', 'kableExtra', 'knitr', 'lobstr', 'lubridate', 'magrittr', 'microbenchmark', 'optparse', 'patchwork', 'peakRAM', 'plotly', 'purrr', 'R6', 'readr', 'readxl', 'renv', 'rmarkdown', 'roxygen2', 'scales', 'shiny', 'showtext', 'stringr', 'sysfonts', 'tibble', 'tictoc', 'tidyr', 'tidyverse')

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('RNASeqPower'), update = TRUE, ask = FALSE)

Install GitHub packages.

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

5 Course materials

Course materials will be made available on https://nbisweden.github.io/raukr-2026/home_contents.html once the workshop begins. You can copy-paste code from the website to your R session.

The two Quarto sessions (10-Aug and 11-Aug) have separate materials and exercise files. See https://cderv.github.io/raukr-2026-quarto/setup.html for what to install and download beforehand.

Alternatively, you can also download/clone the materials from GitHub and run them locally. To do this, go to https://github.com/NBISweden/raukr-2026 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-2026.git

This will create a folder called raukr-2026 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.