Reproducibility Resources
This list provides some links to resources on reproducibility topics, with an emphasis on using git
and performing code review.
Please note, this is not an exhaustive list. It includes multiple types of resources for varying levels of experience, so we would not necessarily recommend every resource here for everyone. Resources are listed by topic and in alphabetical order, not in order of recommendation.
Table of Contents
Git
- Introduction to
git
/GitHub using the command line- Version control with Git - The Carpentries
- Learn Git with Bitbucket Cloud
- Getting started with GitHub
- See sidebar within for all tutorials
- Happy Git and GitHub for the UseR
- This resources additionally introduces how to integration
git
with R/R Markdown workflows
- This resources additionally introduces how to integration
- New to Git - Gitkraken
- Introduction to using the
GitKraken
GUI
- Introduction to using the
- Introduction to Git in VS Code
- Introduction to using
git
via the popular text editor Visual Studio COde
- Introduction to using
- Ten Simple Rules for Taking Advantage of Git and GitHub - PLOS Computational Biology provides recommendations for effectively using
git
and GitHub workflows
Code Review
- Ch 5: “Engaging in Code Review - as an author” from Advanced Reproducibility in Cancer Informatics
- Ch 6: “Engaging in Code Review - as a reviewer” from Advanced Reproducibility in Cancer Informatics
- Code Reviews Done Right: Your Missing Guideline by Mischa Hildebrand
- 10 Methods for In-Depth Code Review by Jonathan Hall
- Best Practices for Peer Code Review
- How about Code Reviews? by Duretti Hirpa and Mark Christian of Slack Engineering
- On Empathy & Pull Requests by Duretti Hirpa and Mark Christian of Slack Engineering
- Comments during Code Reviews by Otaru Babatunde
- Opinionated analysis development by Hillary Parker
Project Organization
- Project Organization for Genomics - The Carpentries
- Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science - PLOS Computational Biology
- Ten Simple Rules for Writing and Sharing Computational Analyses in Jupyter Notebooks - PLOS Computational Biology
Resources in Reproducible Computing
- Collections on Reproducibility - Nature
- Good Enough Practices in Scientific Computing - PLOS Computational Biology
- Guide for Reproducible Research - The Turing Way
- Introduction to Reproducibility in Cancer Informatics course - Informatics Technology for Cancer Research (ITCR)
- Advanced Reproducibility in Cancer Informatics course - ITCR
- Learning Bioinformatics at Home - Harvard Informatics Group
- Reproducibility 4 Everyone
- Reproducibility Standards for Machine Learning in the Life Sciences - nature
- Ten Simple Rules for Quick and Dirty Scientific Programming - PLOS Computational Biology
- Ten Simple Rules for Reproducible Computational Research - PLOS Computational Biology
- protocols.io