Introduction & Setup

Session 1

Mickaël CANOUIL, Ph.D.

pro@mickael.canouil.dev

Independent Contractor

Saturday, the 7th of February, 2026

Introduction

About Me

I am Mickaël CANOUIL, I hold a Ph.D. in Biostatistics, with over a decade of academic experience in the genetics of type 2 diabetes and obesity.
My research has contributed to understanding the genetic and molecular mechanisms underlying metabolic diseases, with publications in leading journals.
Currently, I work as a consultant in biostatistics, applying my expertise to diverse projects in multi-omics and data analysis.
I am also deeply involved in the Quarto ecosystem, developing extensions and tools that enhance reproducibility and scientific communication.
My contributions, including Quarto Wizard and various Quarto extensions, aim to streamline workflows for researchers and data scientists.
You can explore my work on GitHub, my projects, and my publications.

Session 1: Introduction & Setup

Welcome & Overview
- Workshop objectives and participant goals.
- Quarto overview: purpose, strengths, and reproducibility benefits.
- What Quarto is and how it works with Pandoc.
- Brief look at the Quarto Guide.

Installation & Environment Setup
- Installing Quarto (installer, Homebrew, Chocolatey).
- Verify installation with quarto check.
- Quarto as a command-line interface.

Quarto Projects
- Project types: default, website, blog, book, manuscript.
- Creating projects with quarto create project.
- Writing with various editors (VS Code, RStudio, Jupyter, etc.).

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.

Learning Objectives

By the end of this session, participants will be able to:

Explain what Quarto is and how it relates to Pandoc.
Install Quarto and verify the installation.
Create and render different Quarto project types.
Set up an IDE for Quarto development.

What is Quarto?

https://quarto.org/

Purpose

Quarto is an open-source scientific and technical publishing system built on Pandoc:

Multi-language platform supporting Python, R, Julia, and Observable.js.
Creates dynamic, reproducible documents from code and narrative text.
Single-source authoring for articles, websites, books, presentations, and dashboards.

Key Strengths

Multi-format output: Generate HTML, PDF, Word, ePub, and more from one source.

Advanced markdown: Cross-references, equations, citations, callouts, and complex layouts.

Tool flexibility: Works with VS Code, RStudio, JupyterLab, or any text editor.

Project system: Render document collections with shared configurations.

Interactive elements: Embed widgets, Shiny apps, and Observable JS for dynamic content.

Reproducibility Benefits

Embedded computation: Code and results stay together, eliminating copy-paste errors.

Version control friendly: Plain text format works seamlessly with Git.

Transparent workflows: Complete audit trail from data to final output.

Collaborative research: Shared environments and dependencies ensure consistent results.

What is Pandoc?

Pandoc (pandoc.org):

is a free software, released under the GPL by John MacFarlane.
is a command line interface (CLI).
allows to convert to and between multiple formats.
understands Markdown syntax.
understands LaTeX math and macros.
handles citations and bibliographies.

How does Quarto work?

---
init:
  theme: "dark"
  themeCSS: ".label foreignObject, .cluster-label foreignObject { font-size: 90%; overflow: visible; }"
---
flowchart LR
  A1[qmd] --> B1{"R<br>(<code>engine: knitr</code>)"}
  A1[qmd] --> B2{"Python<br>(<code>engine: jupyter</code>)"}
  A1[qmd] --> B3{"Julia<br>(<code>engine: julia</code>)"}
  A2[ipynb] --> B2
  B1 --> C[md]
  B2 --> C[md]
  B3 --> C[md]
  C --> D{"Pandoc"}
  D --> E["HTML"]
  D --> F["Typst"]
  D --> G["Reveal.js"]
  D --> H[...]

  subgraph engine [Engine]
  B1
  B2
  B3
  end

A Guide to Quarto Versions

Quarto follows a versioning scheme similar to Semantic Versioning with three release types: Pre-release, Release Candidate (RC), and Release.

Tip

Always use the latest stable release for production work. See the Quarto Changelog for the full release history.

Getting started

Downloading and installing Quarto

https://quarto.org/

Downloading and installing Quarto

Additionally, you can download and install Quarto using:

Bash

brew install quarto

Screenshot of https://brew.sh/ webpage — https://brew.sh/

PowerShell

choco install quarto

Screenshot of https://community.chocolatey.org/ webpage — https://community.chocolatey.org/

Using GitHub Codespaces

A pre-configured development environment is available via GitHub Codespaces with all required tools pre-installed: Quarto, R, Python, Julia, TinyTeX, and supporting utilities.

Quarto: a command line interface

bash

quarto --help


Usage:   quarto
Version: 1.9.18

Description:

  Quarto CLI

Options:

  -h, --help     - Show this help.                            
  -V, --version  - Show the version number for this program.  

Commands:

  render     [input] [args...]     - Render files or projects to various document types.                 
  preview    [file] [args...]      - Render and preview a document or website project.                   
  serve      [input]               - Serve a Shiny interactive document.                                 
  create     [type] [commands...]  - Create a Quarto project or extension                                
  use        <type> [target]       - Automate document or project setup tasks.                           
  add        <extension>           - Add an extension to this folder or project                          
  update     [target...]           - Updates an extension or global dependency.                          
  remove     [target...]           - Removes an extension.                                               
  convert    <input>               - Convert documents to alternate representations.                     
  pandoc     [args...]             - Run the version of Pandoc embedded within Quarto.                   
  typst      [args...]             - Run the version of Typst embedded within Quarto.                    
  run        [script] [args...]    - Run a TypeScript, R, Python, or Lua script.                         
  list       <type>                - Lists an extension or global dependency.                            
  install    [target...]           - Installs a global dependency (TinyTex or Chromium).                 
  uninstall  [tool]                - Removes an extension.                                               
  tools                            - Display the status of Quarto installed dependencies                 
  publish    [provider] [path]     - Publish a document or project to a provider.                        
  check      [target]              - Verify correct functioning of Quarto installation.                  
  call                             - Access functions of Quarto subsystems such as its rendering engines.
  help       [command]             - Show this help or the help of a sub-command.

Checking Quarto is installed

bash

quarto check

sh

Quarto 1.8.24
[✓] Checking environment information...
      Quarto cache location: /home/vscode/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.3.1: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.8.24
      Path: /opt/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/vscode/.TinyTeX/bin/x86_64-linux
      Version: 2025

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /usr/bin/google-chrome
      Source: PATH

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.13.7
      Path: /usr/local/python/current/bin/python3
      Jupyter: 5.8.1
      Kernels: julia-1.11, python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.5.1
      Path: /opt/R/4.5.1/lib/R
      LibPaths:
        - /home/vscode/R/x86_64-pc-linux-gnu-library/4.5
        - /opt/R/4.5.1/lib/R/library
      knitr: 1.50
      rmarkdown: 2.29

[✓] Checking Knitr engine render......OK

1: Quarto version and dependencies.
2: Tools installed by Quarto (e.g., quarto install).
3: LaTeX installation detected by Quarto.
4: Chromium-based browser installation detected by Quarto.
5: Python installation and computing dependencies detected by Quarto.
6: R installation and computing dependencies detected by Quarto.

Quarto Projects

Creating a new Quarto project

Bash

quarto create project

bash

 ? Type
 ❯ default
   website
   blog
   manuscript
   book
   confluence

Quarto Projects: `default`

Bash

quarto create project default Default

_demo/Default
|-- Default.qmd
`-- _quarto.yml

0 directories, 2 files

Quarto Projects: `default`

_quarto.yml: project configuration file.

Quarto

project:
  title: "Default"

Default.qmd: default Quarto document.

Quarto

---
title: "Default"
---

## Quarto

Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.

Quarto Projects: `website`

Bash

quarto create project website Website

_demo/Website
|-- _quarto.yml
|-- about.qmd
|-- index.qmd
`-- styles.css

0 directories, 4 files

Quarto Projects: `blog`

Bash

quarto create project blog Blog

_demo/Blog
|-- _quarto.yml
|-- about.qmd
|-- index.qmd
|-- posts
|   |-- _metadata.yml
|   |-- post-with-code
|   |   |-- image.jpg
|   |   `-- index.qmd
|   `-- welcome
|       |-- index.qmd
|       `-- thumbnail.jpg
|-- profile.jpg
`-- styles.css

3 directories, 10 files

Quarto Projects: `book`

Bash

quarto create project book Book

_demo/Book
|-- _quarto.yml
|-- cover.png
|-- index.qmd
|-- intro.qmd
|-- references.bib
|-- references.qmd
`-- summary.qmd

0 directories, 7 files

Quarto Projects: `manuscript`

Bash

quarto create project manuscript Manuscript

_demo/Manuscript
|-- _quarto.yml
|-- index.qmd
`-- references.bib

0 directories, 3 files

Screenshot of https://quarto.org/docs/get-started/hello/positron.html webpage

Screenshot of https://quarto.org/docs/get-started/hello/vscode.html webpage

Screenshot of https://quarto.org/docs/get-started/hello/jupyter.html webpage

Screenshot of https://quarto.org/docs/get-started/hello/rstudio.html webpage

https://quarto.org/

Writing using the Visual Editor

POSITRON
VSCODE
RSTUDIO

Screenshot of https://quarto.org/docs/tools/positron/visual-editor.html webpage

https://quarto.org/

Hands-On Exercise: Creating Your First Quarto Project

Exercise Overview

Objective: Create a personal Quarto document that demonstrates basic features, project setup skills, and IDE integration

Example Code: Exercises

bash

tar -xzf "01-exercises.tar.gz" -C "01-introduction-setup"

IDE Configuration

Before starting, ensure your development environment is ready:

VS Code: Install the Quarto extension (Ctrl/Cmd + Shift + X, search “Quarto”).
Positron: Built-in Quarto support is included (no additional extensions needed).
Open the Command Palette (Ctrl/Cmd + Shift + P) and type “Quarto” to verify available commands.

Part 1: Project Creation

Choose Your Adventure: Create a project using the CLI or your IDE.
Explore the project structure in the IDE’s file explorer panel.

Part 2: IDE Features Exploration

Discover your IDE’s Quarto capabilities:

File recognition: Notice .qmd files have distinctive icons and syntax highlighting.
Document outline: Open a .qmd file and check the Outline/Structure panel (shows headings and sections).
Quarto assist panel: Look for a Quarto-specific panel that provides contextual help.
Command palette power: Ctrl/Cmd + Shift + P → type “Quarto” to see all available commands.
Integrated features: Visual editor mode, preview panels, terminal integration.
Smart editing: Try auto-completion in YAML headers, fenced divs, and code blocks.

Part 3: Document Customisation

Modify the main document (index.qmd) to include:

Update the YAML header with your information:

Code

markdown

---
title: "My Quarto Journey"
author: "Your Name"
date: today
editor: visual  # Enables rich editing features
---

Add content to the document body.

Part 4: Rendering

Try different rendering approaches:

Command Line (classic method):
```
bash
```
```
quarto render
```
IDE Integration (modern workflow):
- Command Palette (Ctrl/Cmd + Shift + P) - search for “Quarto Preview” and/or “Quarto Render” commands.
- Use keyboard shortcut if you configured one
- Notice IDE-specific feedback and error handling

Success Criteria

✅ You’ve successfully completed the exercise if you can:

Configure your IDE for optimal Quarto development.
Create a new Quarto project using the CLI or your IDE.
Navigate project files efficiently in your IDE.
Utilise IDE features like syntax highlighting and command palette.
Modify documents with IDE assistance (auto-completion, outline view).
Render documents using both CLI and IDE methods.

Mickaël CANOUIL, Ph.D.

Independent Contractor

pro@mickael.canouil.dev

Introduction & Setup

Introduction

About Me

Session 1: Introduction & Setup

Workshop Objectives

Learning Objectives

What is Quarto?

What is Quarto?

Purpose

Key Strengths

Reproducibility Benefits

What is Pandoc?

How does Quarto work?

A Guide to Quarto Versions

Getting started

Downloading and installing Quarto

Downloading and installing Quarto

Using GitHub Codespaces

Quarto: a command line interface

Checking Quarto is installed

Quarto Projects

Creating a new Quarto project

Quarto Projects: default

Quarto Projects: default

Quarto Projects: website

Quarto Projects: blog

Quarto Projects: book

Quarto Projects: manuscript

Writing with your favourite editor

Writing using the Visual Editor

Hands-On Exercise: Creating Your First Quarto Project

Exercise Overview

Part 1: Project Creation

Part 2: IDE Features Exploration

Part 3: Document Customisation

Part 4: Rendering

Success Criteria

Mickaël CANOUIL, Ph.D.

Quarto Projects: `default`

Quarto Projects: `default`

Quarto Projects: `website`

Quarto Projects: `blog`

Quarto Projects: `book`

Quarto Projects: `manuscript`