Tools for Reproducible Research

Learning Objectives

• Generate reports for your analyses using RMarkdown
• Track changes as you work on files using a version control system called Git (GitHub Desktop tool)
• Collaborate effectively, and disseminate code & other documents using Github

Preparation Requirements

GitHub Desktop

Please download and install GitHub Desktop

Github account

Create an account for yourself on GitHub. Please be sure to select the free/academic account, as this option has more long-term flexibility.

Lessons

1. Making your data analysis reproducible
2. RMarkdown Basics
3. RMarkdown Intermediate
4. What is Version Control
5. Using Git/GitHub Desktop for version control locally
6. Using GitHub for version control “remotely”
7. Managing conflicts with GitHub Desktop
8. Working with commits
9. Using branches for collaboration and version control

Additional Practice

RMarkdown

• Answer key

Resources

R Markdown

• knitr in a knutshell
• knitr book
• knitr examples
• knitr vignettes

GitHub

• Git on the command line
• The Getting Started with GitHub Desktop is a great way to start exploring it’s functionality, and learning more about what Git can do.
• GitHub also provides extensive support in the form of guides and help.
• GitHub Glossary outlines the most commonly used GitHub/Git terminology.
• Software Carpentry’s Version Control with Git
• Data Carpentry for Biologist’s lessons on Version Control
• HBC’s adaptation of Software Carpentry’s Git lessons

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These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.