Git & GitHub, without the headache
A free, beginner-friendly path into version control for the ManyBabies community — built for R-centric, OSF-organized, multi-lab work, with a real focus on analysis code, reproducibility, shared data, and QC. Every link was checked live and is free to use.
Start here by tier
Not sure where to begin? Find your level and do these three things first.
You want to click, not type.
1. GitHub Hello World — 20 min in the browser, no install.
2. GitHub Desktop — commit & push by clicking.
3. Connect GitHub to your OSF project — code next to your data.
You want the mental model + a clean workflow.
1. Happy Git with R — Git from inside RStudio.
2. A workshop — Software Carpentry or a free CodeRefinery session.
3. Learn Git Branching — makes branches finally click.
You want best practices & recovery.
1. Dangit, Git!?! — copy-paste fixes for "I broke it."
2. Git Flight Rules + Pro Git ch. 7 — the deep manual.
3. Fix ugly notebook diffs — nbstripout & Quarto freeze.
Beginner on-ramps (GUI-first)
Get to your first commit and push without typing a single Git command.
GitHub · Interactive tutorial · Free · 20–30 min
Runs entirely in the browser — explicitly "no command line, no install." The lowest-friction first experience.
GitHub · Free desktop app · ~15 min to first commit
Point-and-click commit / push / pull. See the Getting Started docs. 100% GUI, open-source.
GitHub Docs · How-to · Free · 5 min
Edit a README, codebook, or script and commit it straight from the browser's pencil icon.
Atlassian · Illustrated explainer · Free · 15 min
Jargon-light "why version control exists" — good pre-reading to convince skeptics. No commands.
GitKraken · Video series · Free to watch · ~90 min
Visual, concept-first videos.
Heads up: the GitKraken app's free tier is public-repos-only — fine for learning, not for private lab repos.
Git for researchers & reproducibility
Git framed the way ManyBabies already thinks — provenance, reproducibility, open science.
Jenny Bryan · Free online book (CC BY-NC) · modular
The canonical resource for R users who aren't software devs; "Early GitHub Wins" + the RStudio Git pane get you committing from the IDE, no terminal.
Software Carpentry · Free lesson (CC BY) · ~half day
The gold-standard researcher Git lesson; includes an explicit Open Science episode.
Alan Turing Institute · Free handbook (CC BY) · 2–4 h
Why commit history is a scientific record; frames Git in reproducibility terms.
CodeRefinery / NeIC · Free lesson (CC BY)
Rewritten 2024 specifically for researchers, not engineers; companion git-collaborative lesson covers PRs & forks for multi-lab work.
Library Carpentry · Free lesson (CC BY) · ~half day
Gentle, non-coding entry — good for lab managers, RAs, and coordinators.
Lennart Wittkuhn (U Hamburg) · Free online book (CC BY)
The most recently maintained research-oriented Git book; covers GUI alternatives, with quizzes & exercises.
Poldrack Lab · Free handbook
Psychology-native language (preregistration, OSF, open data); T3 chapters reach GitHub Actions / containers.
Jenny Bryan · The American Statistician 72(1):20–27, 2018 · 30–45 min
The best "why bother" read for a stats / R audience.
Access: publisher is paywalled — the linked free PeerJ preprint (#3159) is the one to read.
Vuorre & Curley · AMPPS 2018 · 45–60 min
The only published Git tutorial by and for psychologists, using RStudio's GUI.
Access: publisher (SAGE) paywalled; the linked PsyArXiv preprint is free.
Free courses, webinars & continuing education
Structured, guided learning. There's no formal CEU for Git in psychology — Carpentries & CodeRefinery are the closest research-grade equivalents.
GitHub Education · Interactive, self-paced · Free · <1 h
Bot-guided exercises inside your own repo.
Heads up: if the skills.github.com portal shows a CSS error, open the exercise repo link directly — the exercise itself works.
CodeRefinery / NeIC · Free live online + open recordings
The strongest continuing-ed fit; research-focused. Next runs Sep 22–24 & Sep 29–Oct 1, 2026; recordings CC-licensed.
The Carpentries · Live workshops + free self-study · ~half day
Built for scientists; many universities host free editions, and a consortium member can host one.
Google · Coursera · MOOC · ~20 h
Well-structured video course with hands-on labs.
Access: free to AUDIT — videos free; graded work + certificate are paid. Click "Audit."
Udacity · Video course · Genuinely free · ~4–6 h
One of the few truly free (not just audit) structured courses.
Microsoft Learn · Interactive module · Free · ~1 h 45
Browser-only; the 58-min guided tour suits terminal-phobic T1.
freeCodeCamp · YouTube video · Free · 1 h 8
One-video crash course; easy to drop in a consortium Slack.
Codecademy · Interactive browser sandbox · ~2–4 h
No local install needed.
Access: freemium — core lessons free; certificate / AI / some projects need a paid plan.
Center for Open Science · Free live webinar + recordings · ~1 h/mo
Not Git per se, but covers OSF↔GitHub linking, preregistration, and data sharing — your ecosystem.
Notebooks & analysis-code version control
The fix for ugly, unreviewable diffs from .ipynb, .Rmd, and .qmd files.
Jenny Bryan · Ch. 12 · Free book chapter · 30–45 min
The canonical RStudio Git-pane setup; commit / push from the IDE, no terminal.
Jenny Bryan · Ch. 18 · Free chapter · 30 min
Use output: github_document so .Rmd diffs show readable Markdown, not HTML blobs.
Posit · Tool docs · Free · 20 min
freeze: auto version-controls outputs so collaborators don't re-run expensive code → stable, reviewable diffs.
Jupyter Project · Tool docs · Free (MIT)
Cell-level, content-aware diffs + a visual mergetool; auto-resolves execution-count conflicts. The fix for Jupyter merge hell.
Open source · Git filter / pre-commit hook · Free · 15 min
A one-time nbstripout --install keeps multi-MB outputs & images out of Git; optional Action enforces clean notebooks on PRs.
Open source · Tool docs · Free
Pair .ipynb with a .py/.md so you commit a diff-friendly script; supports the Quarto Markdown format.
ReviewNB · GitHub app · Free for public/academic repos
Rendered, cell-level notebook diffs + inline comments inside PRs.
Heads up: private repos capped (10 PR/mo) — but ManyBabies public repos get unlimited free use.
Toptal · Web tool · Free · 5 min
Generate a correct .gitignore for R, Python, JupyterNotebook, RStudio — stops accidental .RData / __pycache__ / .ipynb_checkpoints commits.
GitHub · Reference (CC0)
The authoritative R and Python templates GitHub pre-populates; customize (e.g., add _freeze/ for Quarto).
Google · Interactive · Free w/ Google login · 20–30 min
Open / commit notebooks to a GitHub repo from Colab, no local setup.
Heads up: needs a Google account; pair the repo with nbstripout (Colab won't fix diffs itself).
Shared datasets, data collection & QC workflows
When plain Git is the wrong tool for big/binary data — and how to run QC through GitHub.
Turing Institute · Free chapter · 20–30 min
Read this first: why plain Git fails for large/binary data, and Git LFS vs git-annex vs DataLad. The conceptual bridge.
GitHub · Tool · Free · 15 min
Version big files via pointers + .gitattributes. Good for modest files.
Heads up: GitHub's free LFS quota is ~1 GB storage/bandwidth — for large data prefer DataLad/GIN or OSF.
GitHub Docs · Reference · 10 min
Per-file ceilings (2 GB Free/Pro) and quotas — read before betting your data architecture on LFS.
DataLad community · Free book
The most thorough resource for distributed multi-lab data: nested datasets (one per site), provenance, on-demand retrieval, sensitive-data collaboration. Big files never enter the Git store.
DataLad · Free (BSD)
Standard in open neuroscience (OpenNeuro / NEMAR); publishes to GitHub, S3, Figshare. Pair with GIN (gin.g-node.org) — free academic storage.
Iterative · Tool docs · Free/OSS · 30–60 min
Lighter-weight alternative to DataLad for Python-comfortable labs; also versions ML pipelines; has a VS Code extension.
Center for Open Science · Workflow guide · Free · 15 min
Because ManyBabies lives on OSF: link the analysis repo to the OSF project in the browser so code sits beside preregistrations + data.
GitHub Docs · Reference/workflow · Free · 20–30 min
Turn GitHub into a data-QC tracker: an Issue per lab anomaly, a Projects board to track which sites passed QC.
GitHub Docs · Reference · Free · 10–15 min
Data QC as code review: gate incoming data/scripts with comment / approve / request-changes + CODEOWNERS auto-assignment — auditable quality control.
GitHub · Docs · Free for public repos · 30–60 min
Auto-run a validate_data.R on every PR and post a pass/fail check before a human looks. Scales QC across dozens of sites.
The consortium · Public org · all tiers
Your own best teacher: browse mb1-analysis-public & mb2-analysis (real collaborative R analysis), mb3-rules, the validator Shiny data-upload QC app, and mb1-cdi-followup. Real, domain-native models.
Cheat sheets, best practices & rescue
For the "I use Git and it keeps biting me" crowd — undo mistakes, fix conflicts, recover lost work.
Katie Sylor-Miller · Recovery cookbook · Free · skim 10–15 min
Scenario-first fixes anchored on git reflog. Use the clean-language dangitgit.com mirror in training materials. (original here.)
k88hudson · Recovery cookbook (CC BY-SA) · reference
The most comprehensive "things went wrong" manual (42k★, maintained 2026): bad merges, lost commits, accidental force-push, rebase disasters.
Chacon & Straub · Free book (CC)
The authoritative reference; Ch. 2.4 (Undoing Things) and Ch. 7 (Reset Demystified, Advanced Merging, rerere, Stashing) explain the why.
Atlassian · Tutorials · Free
Best diagrams for reset vs checkout vs revert, and a reflog deep-dive.
Peter Cottle · Interactive visualizer · Free/OSS · 1–4 h
Watch the commit graph move — the fastest way to truly understand branches, merges, and rebase (the root of most T3 pain).
GitHub Education · 2-page printable · Free
Pin it above your desk: setup, staging, branching, remotes, stash, reset.
Chris Beams · Article · Free · 15–20 min
The seven rules; clean history = a reproducibility record.
Community spec · Free · 15 min
feat/fix/docs… types map cleanly to data-cleaning, analysis updates, and pipeline changes; enables auto-changelogs.
GitHub Docs · Workflow guide · Free · 10 min
The branch → PR → review → merge loop multi-lab projects run on; bridges OSF-only users into PRs.
ManyBabies-specific notes
- Learn from your own repos. github.com/manybabies is public — point trainees at
mb1-analysis-public,mb2-analysis,mb3-rules, thevalidatorShiny QC app, andmb1-cdi-followup. Domain-native examples beat generic dev tutorials. - OSF is the hub. Connect each analysis repo to its OSF project (browser, no terminal) so versioned code sits beside preregistrations and data.
- A workable consortium workflow. Contributors branch → open a PR → a data coordinator reviews (data QC = code review) → merge. One Issue per lab anomaly, a Projects board to track which sites cleared QC, and a GitHub Action to auto-run validation on every PR.
- Don't put raw infant data or large binaries in plain Git. Small files → Git LFS (mind the ~1 GB free cap). Large or many files → DataLad + GIN (free for academics) or keep data on OSF Storage and commit code + pointers.
- Keep notebooks reviewable.
nbstripoutfor Jupyter;output: github_documentfor.Rmd;freeze: autofor Quarto — otherwise PRs are unreadable.
Appendix — one-page everyday Git
The everyday loop
git clone <url> # get a repo (once)
git status # what changed?
git pull # get teammates' latest BEFORE you start
git add <file> # stage a change (git add -A = everything)
git commit -m "message" # save a snapshot
git push # share itBranching — the safe way to work
git switch -c my-analysis # create + move to a new branch
git switch main # move back
# then open a Pull Request on GitHub to merge"I broke something" — don't panic
git restore <file> # discard unstaged changes to a file
git restore --staged <file> # unstage (keep the edits)
git reflog # find lost commits — your time machineWhen in doubt: dangitgit.com or the printable cheat sheet. In R? Do all of this from the RStudio Git pane (Happy Git ch. 12).
Verification & access caveats
All resources were checked against their live source in June 2026 and are free to use. Most are confirmed live & free with no caveats — these carry one worth knowing.
| Resource | Status | Caveat / note |
|---|---|---|
| GitHub Skills | Confirmed* | Portal may throw a CSS error — open the exercise repo directly. Exercises work. |
| GitKraken (app) | Partial | Free tier is public-repos-only; private repos need a paid plan / student pack. Videos are free. |
| Google "Intro to Git/GitHub" (Coursera) | Confirmed | Free to audit only — videos free; graded work + certificate are paid. |
| Codecademy Learn Git | Confirmed | Freemium — core lessons free; certificate / AI / some projects are paid. |
| ReviewNB | Confirmed | Free & unlimited for public/academic repos; private capped at 10 PR/mo. ManyBabies public repos = fine. |
| Google Colab ↔ GitHub | Partial | Requires a Google login; GPU/TPU is freemium. Integration confirmed via source repo. |
| Git LFS (on GitHub) | Confirmed | Tool free; GitHub storage/bandwidth capped at ~1 GB free — use DataLad/GIN or OSF for large data. |
| Bryan, "…Version Control?" (paper) | Partial | Publisher paywalled; the linked free PeerJ preprint (#3159) is the one to read. |
| Vuorre & Curley tutorial (paper) | Confirmed | Publisher (SAGE) paywalled; the linked PsyArXiv preprint is free. |
| Connect GitHub to OSF (help article) | Partial | Exact article restructured into the OSF Add-ons guide; workflow confirmed present. |
| Happy Git with R | Confirmed | Live & free; if a chapter link misbehaves, navigate from the table of contents. |
- GitHub Learning Lab → migrated to GitHub Skills; old URLs are dead.
- rOpenSci Reproducibility Guide → archived/stale (no Quarto/renv).
- PeerJ Preprints → closed to new submissions in 2019 (static archive; the Bryan preprint still loads).
- Git-it desktop app → unmaintained since 2017.
- LinkedIn Learning "Git Essential Training" → only conditionally free via a library login.
- Coursera / DataCamp data-science Git courses → paid or audit-gated lab exercises.