This two-part series introduces Zotero, a free reference management tool, and demonstrates its integration into reproducible research workflows. Part 1 covers essential features for organizing literature and citing sources in traditional word processors. Part 2 addresses advanced integration with RStudio, RMarkdown, and Quarto for computational research. Each one hour and 15 minutes training includes hands-on practice. No prior experience with Zotero is required.
This one hour and half- hands-on training that teaches participants how to integrate Zotero references into reproducible scientific documents written in RStudio using Quarto. Participants learn how to set up citation workflows, insert and manage references, generate bibliographies, cite software and R packages, and produce publication-ready documents in multiple formats. This training focuses on practical, reproducible writing techniques used in modern computational research.
By the end of this training, attendees will be able to:
- Explain how Quarto, Pandoc, and BibTeX work together.
- Configure Zotero and Better BibTeX to keep a .bib file in sync.
- Insert and manage citations using RStudio’s Visual Editor.
- Apply citation styles to format bibliographies.
- Cite R and R packages to support reproducible research.
This training assumes participants have completed Part 1: Zotero Fundamentals or have equivalent experience using Zotero.
To participate fully in the hands-on portion, attendees should also:
- Installed the most recent versions of R and RStudio
- Zotero must be installed and running during the session.
- Have a basic working knowledge of RStudio, including opening projects.
- Review our Data Services: On-Demand Content on RStudio Projects and R Fundamentals (recommended for newer users).
The following files can be downloaded from the NIH Library GitHub:
2025-nature-sarnataro.qmd, mocked-up Quarto doc.
sarnataro-ids.txt, contains DOIs.