Writing Reproducible Manuscripts in R & Python


Research Data Management Support
Utrecht University


February 23, 2024


Open Science practices are becoming central to the way research is conducted. In this workshop, you will learn to set up a reproducible workflow to create a publication-ready manuscript that combines data, R or Python code, text, and references.

We will use the Quarto publishing system in conjunction with R or Python to create a publication-ready manuscript that combines data, code, text, and references. More specifically, you will learn how to:

  • Create a reproducible project (folder) structure
  • Use Markdown syntax effectively for writing text
  • Run analyses in code chunks or cells
  • Manage references using Zotero and Better BibTex for Zotero
  • Render your Quarto project to docx, HTML, and pdf files

This workflow reduces the amount of human error, improves computational reproducibility and makes updating your scientific manuscript more efficient.

By the end of the workshop, you will be sufficiently familiar with the tools and components behind a reproducible manunscript, so you can implement the workflow in your own research projects.

Our workshop material is licensed under a Creative Commons Attribution 4.0 International License. You can view the license on our GitHub repository.