Tools for Transparent Research – Hands-On with Git & RMarkdown
Have you struggled to reproduce your own results or those of others? Does it seem like you know about the reproducibility tools that are out there, but you need some help to navigate them better? Come join the HBC for a series of hands-on workshops aimed at our recommended practices for reproducible research.
First workshop of the series:
- WHO? Free to all Harvard affiliates
- WHAT? R Basics
- WHERE? Register for zoom link
- WHEN? Wednesday, February 19, 2025, from 1-4pm
- Pre-requisite: None, but R Basics is required for the March session, Reproducible Research using Rmarkdown
- Setup: All workshops are hands-on and require you to have a computer available.
- R Basics: R is a simple programming environment that enables the effective handling of data, while providing excellent graphical support. RStudio is a tool that provides a user-friendly environment for working with R. This workshop gives participants an overview of the basics of the R programming language and RStudio. Setup instructions will be provided to those who register.
- The Winter 2025 workshops are listed in the table below, along with registration links and prerequisites. All workshops are currently held remotely via Zoom.
Current Topics in Bioinformatics Upcoming Schedule: (Free, hands-on workshops available to all Harvard affiliates)
| Topic | Date | Time | Register | Pre-requisites |
| R basics | 2/19/25 | 1 – 4pm | Sign up! | None |
| RMarkdown for Reproducible Reporting | 3/19/25 | 1 – 4pm | Sign up! | R basics or Online R resource from Harvard Catalyst |
| “Track Changes” for your code: An Introduction to Git and GitHub | 4/16/25 | 1 – 4pm | Sign up! | None |
| Coding with others: Managing conflicts on GitHub | 5/21/25 | 1 – 4pm | Sign up! | “Track Changes” for your code: An Introduction to Git and GitHub |
Workshop descriptions
R Basics: R is a simple programming environment that enables the effective handling of data, while providing excellent graphical support. RStudio is a tool that provides a user-friendly environment for working with R. This workshop gives participants an overview of the basics of the R programming language and RStudio.
RMarkdown for Reproducible Reporting: Integrating your R data analyses into a report format allows for easy retrieval of the packages/versions and code used to generate your results and figures. It allows for efficient communication of your results with your collaborators. The knitr R package allows for the easy generation of professional reports for any R analysis, while allowing for customization and easy revision. In this 3-hour workshop, we will cover the simple RMarkdown syntax and explore options for customizing your reports. The R Basics workshop from February, or a working knowledge of R, is a pre-requisite for this workshop.
“Track Changes” for your code: An Introduction to Git and GitHub: Version control is the process of managing changes to files over time and implementing robust version control practices into your analyses can help make your work easier to share, integrate contributions from others and revert to previous versions. Git, and its associated hosting platform GitHub, has emerged as one of the foremost version control tools within academia and industry. In this 3-hour workshop, we will introduce the concept of version control, use the GitHub Desktop interface to manage files between local and remote repositories and interact with files on GitHub.
Coding with others: Managing conflicts on GitHub: One of the strengths of GitHub is the ability to share and collaborate on code with others. Sometimes in this process you and your collaborator may each make adjustments to the code that impacts each other and this “conflict” will need to be adjudicated. Or you will want to be working on developing the next version of your software with your collaborator and want a space with the functionality of version control to do this. In this 3-hour workshop, we will build upon our previous “Track Changes” for your code: An Introduction to Git and GitHub workshop to discuss how to resolve conflicts on GitHub, edit commits and create branches to manage developmental code.