Reproducibility with Git and Quarto

Genomics Aotearoa

This two-part workshop introduces new users to key tools and concepts which support reproducibility in data science: Git/GitHub and Quarto.

Online

This online workshop will be taught on Thursday the 23rd and Friday 24th of October, 2025 from 9:30am-2:30pm NZT each day. The workshop is for New Zealand researchers who want to make their workflows more reproducible.This two-day workshop will show you not only how to make your research more reproducible, but also how to more easily collaborate on projects with other researchers and how to generate polished reports to share with others.With Git and GitHub, you’ll learn how to manage and host your own code, and how to download, adapt, and build on code that others share - whether that’s custom scripts, small programs, or entire projects.Using Quarto, you’ll then learn how to turn your analysis into clear, self-contained documents, create polished HTML outputs with embedded results, and publish your work online as a website. Some of the topics covered in this workshop are:<ul><li>An introduction to Git and GitHub</li><li>Setting up a git repository</li><li>Tracking all changes in your work over time</li><li>An introduction to Quarto for documenting work</li><li>Creating documents - pdf, websites, slideshows</li><li>Executable code blocks within your documents </li></ul> PrerequisitesThis is an intermediate level workshop. We assume the learner has no prior experience with the tools covered in the workshop, but you must have attended our <a href="https://genomicsaotearoa.github.io/BioinformaticsTrainingProgramme/portfolio.html#introduction-to-the-r-programming-language" title="https://genomicsaotearoa.github.io/BioinformaticsTrainingProgramme/portfolio.html#introduction-to-the-r-programming-language" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">Introduction to R workshop </a>and <a href="https://genomicsaotearoa.github.io/BioinformaticsTrainingProgramme/portfolio.html#introduction-to-shell" title="https://genomicsaotearoa.github.io/BioinformaticsTrainingProgramme/portfolio.html#introduction-to-shell" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">Introduction to Shell workshop</a>, or have equivalent experience. You should be comfortable navigating the file system on your own computer using commands such as cd, pwd and ls and be comfortable with basic R/RStudio syntax (e.g., know what functions, objects and vectors are, and have used RStudio before). SetupThis is a fully online, hands-on workshop. Note that all work will be done on your local computer, so you will need to complete these steps before attending the workshop:<ul><li>Install the latest version of R and RStudio.</li><li>Install Git</li><li>Make a GitHub account</li></ul>Detailed <a href="https://genomicsaotearoa.github.io/reproducibility_with_git_and_quarto/git_overview.html#setup-on-local-machine" title="https://genomicsaotearoa.github.io/reproducibility_with_git_and_quarto/git_overview.html#setup-on-local-machine" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">set-up instructions can be found here.</a>You can preview the <a href="https://genomicsaotearoa.github.io/reproducibility_with_git_and_quarto/" title="https://genomicsaotearoa.github.io/reproducibility_with_git_and_quarto/" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">workshop material here.</a>If you need guidance or assistance with completing these steps, you can contact chloe.vanderburg@otago.ac.nz and arrange to attend an online set-up session taking place on 16th-17th October 2025. Participants must have their own laptops and plan to participate actively. You will require a working web browser. If you have any questions about these workshops, including whether they are suitable for you, please contact chloe.vanderburg@otago.ac.nz

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Reproducibility with Git and Quarto

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Reproducibility with Git and Quarto

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