A list of resources for reproducible research. I work primarily with R, so these resources are selected with that in mind. This list is a work in-progress.

Basic resources

• RStudio - an IDE for R that facilitates projects
• Quatro - an open-source scientific and technical publishing system
• renv - an R package for managing project dependencies
• GitHub - a web-based platform for version control and collaboration
• Binder - a web-based platform for creating interactive computational environments from code repositories
• OSF - the Open Science Framework, a free and open-source project management tool for researchers
• Docker - a platform for building, packaging, and distributing applications as containers
• rang - reconstruct reproducible R environments from older projects
• groundhog - load or install R packages available at a specific date
• fusen - build an R package from an Rmarkdown file
• targets - an R package for creating pipelines for data science
• gert - a simple git client for R

An overview of R packages related to reproducible research can be found here.

Quatro

• awesome-quarto - A curated list of resources and tools for using Quarto, a document automation tool for reproducible research

Example research projects built with Quarto

• self-reference - a master's thesis on the Self Reference Effect written in Quarto
• indo-rct - a reproduction of a traditionally published paper using Quarto

Misc

• Project-oriented workflows - a chapter on why to use RStudio projects
• Project-oriented workflows - a similar blogpost
• Overview of reproducible research - a book chapter on the whys and hows of reproducible research
• The Turing Way guide to reproducible research - a guide to reproducible research
• Quality assurance of code for research - an online book with many resources on code quality and reproducibility
• command-line-args - a tutorial on how to run R scripts with different input arguments via the command line
• Docker 101 for Data Scientists - a tutorial on Docker for data scientists
• RStudio projects workflow
• Happy Git and GitHub for the useR - a resource for learning how to use Git and GitHub effectively in conjunction with the R programming language.
• Reproducible pipelines - a book on building reproducible analytical pipelines with R
• r-pkgs - a book on developing R packages
• Research projects as R packages - a blog post about why and how you might create an R package for a data analysis project
• Reproducible research in psychology with Quarto - a blog post about using Quarto for research projects
• Targets works - a series of articles detailing an example use of the targets package
• Reproducible computation at scale in R with targets - a github repo with a workshop tutorial gradually building larger targets pipelines
• Another example of targets - a blog post about using the targets package for a data analysis project
• Common setup tasks for R projects