Mastering Quarto CLI: From Authoring to Publishing

Dates

5th-6th February 2026

To foster international participation, this course will be held online

 

Course overview

 

This workshop offers a comprehensive, hands-on exploration of the Quarto ecosystem, designed to equip participants with the skills needed to create reproducible documents and interactive publications. Through a series of interactive sessions, attendees will learn fundamental Markdown techniques, integrate executable code in various programming languages, and experiment with different output formats. The agenda covers installation, authoring essentials, code embedding, publishing strategies, and advanced formatting techniques to help learners develop polished, professional projects.  

Workshop Objectives

  • Familiarise participants with the Quarto ecosystem.
  • Empower attendees to create reproducible documents and interactive publications.
  • Guide learners through embedding code, adjusting outputs, and publishing projects.
  • Encourage hands‑on practice with interactive sessions.

Prerequisites

Prior to the workshop, please ensure you have the following installed on your computer.  

  • Quarto CLI 1.7.26 or higher: https://quarto.org/docs/get-started 
  • R 4.5.* or higher: https://cran.r-project.org
  • Python 3.13.* or higher: https://www.python.org/downloads/
  • Julia 1.11.* or higher: https://julialang.org/downloads/

Alternatively, you can use GitHub Codespaces

./.devcontainer/setup.sh --what <all|r|python|julia>

 

Session content

Day 1: 14:00 – 17:00 Berlin time


Session 1: Introduction & Setup

  • Welcome & workshop objectives

  • Quarto overview: purpose, strengths, reproducibility benefits

  • Installation & environment setup (R, Python, Julia)

  • Quarto project types and editors (VS Code, RStudio, Jupyter)

Session 2: Authoring Essentials

  • Markdown fundamentals: headings, lists, links, tables, math, code blocks

  • Quarto-specific features: callouts, Mermaid diagrams, cross-references

  • YAML configuration and multi-format output

Session 3: Embedding Computations & Code

  • Setting up computing environments and multi-language workflows

  • Execution options, caching, and freeze management

  • Dynamic documents with parameters


Day 2: 14:00 – 17:00 Berlin time


Session 4: Formats & Projects

  • Project architecture and structure for websites, blogs, manuscripts, books

  • Multi-format output optimization and resource management

  • Custom formats and advanced project features

Session 5: Advanced Formatting & Branding

  • Document layout customization, themes, and SCSS

  • Brand identity: logos, color schemes, typography, reusable templates

  • Integrating CSS/JS for responsive, branded projects

Session 6: Publishing

  • Publishing options: Quarto Pub, GitHub Pages, Netlify

  • Deployment workflows, version control, and automated publishing

  • Advanced topics: custom domains, CI workflows, troubleshooting

Session 7: Closing & Next Steps

  • Recap of key learning outcomes

  • Resources for further learning

  • Participant feedback and discussion

Instructor

 

 

Dr. Mickaël CANOUIL  

 

His research has contributed to understanding the genetic and molecular mechanisms underlying metabolic diseases, with publications in leading journals. Currently, he works as a consultant in biostatistics, applying my expertise to diverse projects in multi-omics and data analysis. He is also deeply involved in the Quarto ecosystem, developing extensions and tools that enhance reproducibility and scientific communication. His contributions, including Quarto Wizard and various Quarto extensions, aim to streamline workflows for researchers and data scientists.

 


COst overview

 

Package 1

 

 

 

280 €

 

 

 

 

 

 

 

 

 


Cancellation Policy:

 

> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.

 

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.