RaukR 2026 · Quarto

Two Quarto sessions at RaukR 2026 — the Advanced R for Bioinformatics summer school (Visby, Gotland; NBIS / SciLifeLab / Uppsala University), 10–11 Aug 2026.

Two afternoon sessions on writing and publishing with Quarto, for an audience that already writes R and has met R Markdown or Quarto. The angle is what Quarto is as a system, and how to go from a single document to a whole project you can publish — not "what is a code chunk".

• Instructor: Christophe Dervieux (Posit — R Markdown / Quarto)
• Day 1 · Mon 10 Aug — Introduction to Quarto: the single document — authoring, layout, and the modern output story (including Typst).
• Day 2 · Tue 11 Aug — Quarto projects: beyond one file — websites, config, publishing, tips & tricks.

Each day is two parts with a gap (150 min on Day 1, 180 on Day 2), and each part reaches a hands-on payoff. The running example is the base-R penguins dataset (R ≥ 4.5), used in every example across both days.

The site

The site is live at https://cderv.github.io/raukr-2026-quarto/.

This repository is a Quarto website project; the rendered slides, labs, and setup page are its output, published to the gh-pages branch with just publish gh. The material is still being authored, so pages may change up to the school.

Before you arrive

The sessions are hands-on, so come with a working toolchain: R ≥ 4.5, Quarto ≥ 1.9 (the Typst article layout used on Day 1 landed in 1.9), and an editor with Quarto support (Positron, VS Code, or RStudio). Typst (the modern PDF path used on Day 1) ships inside Quarto, so there is nothing extra to install.

Full instructions, including how to recreate the exact R environment, are on the Setup page (setup.qmd, rendered on the site above). This repo pins its R dependencies with renv:

renv::restore()   # recreate the environment from renv.lock

Programme

Day	Session	Slides	Lab
Mon 10 Aug	Introduction to Quarto — authoring, layout, and the output story (including Typst)	slides/quarto/	labs/quarto/
Tue 11 Aug	Quarto projects — websites, config, publishing, tips & tricks	slides/quarto-projects/	labs/quarto-projects/

What's in this repo

index.qmd · setup.qmd     Home page and setup instructions
slides/quarto/            Day 1 — Introduction to Quarto (revealjs deck)
slides/quarto-projects/   Day 2 — Quarto projects (revealjs deck)
labs/quarto/              Day 1 lab, with exercise files and demos
labs/quarto-projects/     Day 2 lab, with a starter and a worked solution
exercises/                Generated participant files (see below) — never hand-edited
tools/                    R scripts that generate the exercises repo and the demo pages
_quarto.yml · _brand.yml  Website config and branding
justfile                  Build entry point

The exercises run on the base-R penguins dataset, with solutions available in each lab.

Participant materials live in a separate repo. labs/ is the source of truth here. just exercises regenerates the exercises/ files via tools/sync-exercises.R, and just publish-exercises mirrors it to cderv/raukr-2026-quarto-exercises, the repo participants download with usethis::use_course(). Never hand-edit exercises/. A CI drift-guard enforces that it matches labs/.

How this was built

The teaching is Christophe's: what belongs in two afternoons, what an experienced-R audience can skip, which Quarto claims are safe to make on stage.

Drafting and review were LLM-assisted, session by session and directed throughout. The working setup is in the open under .claude/: path-scoped gotchas that bite when editing (rules/), reference notes on the Quarto techniques used here (references/), a four-lens review panel and an agent that walks the labs as a first-time participant (agents/, commands/), the Quarto bug reports this material turned up (upstream-issues/), and two Claude Code hooks (sandbox setup, and a commit block on a stale _freeze/). Useful if you're adapting this workshop.

Building it

The justfile is the build entry point (run just for the list):

just render     # render the whole site to _site/, then the demo documents
just preview    # live preview with auto-reload
just demos      # render the finished lab documents to _site/demos/
just clean      # remove build artifacts
just publish gh # render, then publish to GitHub Pages (or: just publish connect)

just demos renders the finished lab documents (the Day-1 results and the Day-2 website) via tools/render-demos.R, so they can be shown from a URL during the sessions. They are deployed but not linked from the site, and just render runs them, so publishing includes them.

just publish gh pushes the rendered _site/ to the gh-pages branch and prints the live URL (https://cderv.github.io/raukr-2026-quarto/) when it finishes.

_freeze/ is versioned: after editing an executable .qmd, re-render it (quarto render <file>) and commit the refreshed freeze so the site builds on CI without re-running R.

Prior art

This material builds on Christophe's earlier Quarto talks and tutorials, updated for 2026: RaukR 2025, useR! 2024 tutorial, RR 2023, and RR 2026 (Typst).

License

See LICENSE.md:

• Content — text, slides, exercises, pages, figures: CC BY 4.0.
• Code — scripts, build config, authoring tooling: MIT.

This content is authored so it can later be folded into the NBIS RaukR site; how that material relates to this one (CC BY-NC-SA, referenced not vendored) is covered in LICENSE.md.