Work in progress. This is not meant to be a polished guide for everyone. It's mostly a summary of how I've been using Claude Code for academic work — creating lecture slides, writing R scripts, managing Beamer-to-Quarto workflows, and so on. I keep learning new things, and as I do, I keep updating these files. This is just a way for me to share what I've figured out with friends and colleagues.
Live site: eyangs.github.io/claude-code-my-workflow
A ready-to-fork starter kit for academics using Claude Code with LaTeX/Beamer + R + Quarto. You describe what you want; Claude plans the approach, runs specialized agents, fixes issues, verifies quality, and presents results — like a contractor who handles the entire job. Extracted from a production PhD course (6 lectures, 800+ slides).
# Fork this repo on GitHub (click "Fork" on the repo page), then:
git clone https://github.com/YOUR_USERNAME/claude-code-my-workflow.git my-project
cd my-projectReplace YOUR_USERNAME with your GitHub username.
claudeUsing VS Code? Open the Claude Code panel instead. Everything works the same — see the full guide for details.
Then paste the following, filling in your project details:
I am starting to work on [PROJECT NAME] in this repo. [Describe your project in 2–3 sentences — what you're building, who it's for, what tools you use.]
I want our collaboration to be structured, precise, and rigorous. When creating visuals, everything must be polished and publication-ready.
I've set up the Claude Code academic workflow (forked from
pedrohcgs/claude-code-my-workflow). The configuration files are already in this repo. Please read them, understand the workflow, and then update all configuration files to fit my project — fill in placeholders inCLAUDE.md, adjust rules if needed, and propose any customizations specific to my use case.After that, use the plan-first workflow for all non-trivial tasks. Once I approve a plan, switch to contractor mode — coordinate everything autonomously and only come back to me when there's ambiguity or a decision to make.
Enter plan mode and start by adapting the workflow configuration for this project.
What this does: Claude reads all the configuration files, fills in your project name, institution, and preferences, then enters contractor mode — planning, implementing, reviewing, and verifying autonomously. You approve the plan and Claude handles the rest.
Prefer to configure manually? See the full guide for step-by-step manual setup instructions.
You describe a task. Claude plans the approach, implements it, runs specialized review agents, fixes issues, re-verifies, and scores against quality gates — all autonomously. You see a summary when the work meets quality standards. Say "just do it" and it auto-commits too.
Instead of one general-purpose reviewer, 10 focused agents each check one dimension:
- proofreader — grammar/typos
- slide-auditor — visual layout
- pedagogy-reviewer — teaching quality
- r-reviewer — R code quality
- domain-reviewer — field-specific correctness (template — customize for your field)
Each is better at its narrow task than a generalist would be. The /slide-excellence skill runs them all in parallel.
Two agents work in opposition: the critic reads both Beamer and Quarto and produces harsh findings. The fixer implements exactly what the critic found. They loop until the critic says "APPROVED" (or 5 rounds max). This catches errors that single-pass review misses.
Every file gets a score (0–100). Scores below threshold block the action:
- 80 — commit threshold
- 90 — PR threshold
- 95 — excellence (aspirational)
For a comprehensive walkthrough, read the full guide (or see the source).
It covers:
- Why This Workflow Exists — the problem and the vision
- Getting Started — fork, paste one prompt, and Claude sets up the rest
- The System in Action — specialized agents, adversarial QA, quality scoring
- The Building Blocks — CLAUDE.md, rules, skills, agents, hooks, memory
- Workflow Patterns — lecture creation, translation, replication, multi-agent review, research exploration
- Customizing for Your Domain — creating your own reviewers and knowledge bases
10 agents, 19 skills, 17 rules, 4 hooks (click to expand)
| Agent | What It Does |
|---|---|
proofreader |
Grammar, typos, overflow, consistency review |
slide-auditor |
Visual layout audit (overflow, font consistency, spacing) |
pedagogy-reviewer |
13-pattern pedagogical review (narrative arc, notation density, pacing) |
r-reviewer |
R code quality, reproducibility, and domain correctness |
tikz-reviewer |
Merciless TikZ diagram visual critique |
beamer-translator |
Beamer-to-Quarto translation specialist |
quarto-critic |
Adversarial QA comparing Quarto against Beamer benchmark |
quarto-fixer |
Implements fixes from the critic agent |
verifier |
End-to-end task completion verification |
domain-reviewer |
Template for your field-specific substance reviewer |
| Skill | What It Does |
|---|---|
/compile-latex |
3-pass XeLaTeX compilation with bibtex |
/deploy |
Render Quarto + sync to GitHub Pages |
/extract-tikz |
TikZ diagrams to PDF to SVG pipeline |
/proofread |
Launch proofreader on a file |
/visual-audit |
Launch slide-auditor on a file |
/pedagogy-review |
Launch pedagogy-reviewer on a file |
/review-r |
Launch R code reviewer |
/qa-quarto |
Adversarial critic-fixer loop (max 5 rounds) |
/slide-excellence |
Combined multi-agent review |
/translate-to-quarto |
Full 11-phase Beamer-to-Quarto translation |
/validate-bib |
Cross-reference citations against bibliography |
/devils-advocate |
Challenge design decisions before committing |
/create-lecture |
Full lecture creation workflow |
/commit |
Stage, commit, create PR, and merge to main |
/lit-review |
Literature search, synthesis, and gap identification |
/research-ideation |
Generate research questions and empirical strategies |
/interview-me |
Interactive interview to formalize a research idea |
/review-paper |
Manuscript review: structure, econometrics, referee objections |
/data-analysis |
End-to-end R analysis with publication-ready output |
| Feature | What It Does |
|---|---|
| Exploration folder | Structured explorations/ sandbox with graduate/archive lifecycle |
| Fast-track workflow | 60/100 quality threshold for rapid prototyping |
| Simplified orchestrator | implement → verify → score → done (no multi-round reviews) |
| Enhanced session logging | Structured tables for changes, decisions, verification |
| Merge-only reporting | Quality reports at merge time only |
| Math line-length exception | Long lines acceptable for documented formulas |
| Workflow quick reference | One-page cheat sheet at .claude/WORKFLOW_QUICK_REF.md |
Rules use path-scoped loading: always-on rules load every session (~100 lines total); path-scoped rules load only when Claude works on matching files. Claude follows ~150 instructions reliably, so less is more.
Always-on (no paths: frontmatter — load every session):
| Rule | What It Enforces |
|---|---|
plan-first-workflow |
Plan mode for non-trivial tasks + context preservation |
orchestrator-protocol |
Contractor mode: implement → verify → review → fix → score |
session-logging |
Three logging triggers: post-plan, incremental, end-of-session |
Path-scoped (load only when working on matching files):
| Rule | Triggers On | What It Enforces |
|---|---|---|
verification-protocol |
.tex, .qmd, docs/ |
Task completion checklist |
single-source-of-truth |
Figures/, .tex, .qmd |
No content duplication; Beamer is authoritative |
quality-gates |
.tex, .qmd, *.R |
80/90/95 scoring + tolerance thresholds |
r-code-conventions |
*.R |
R coding standards + math line-length exception |
tikz-visual-quality |
.tex |
TikZ diagram visual standards |
beamer-quarto-sync |
.tex, .qmd |
Auto-sync Beamer edits to Quarto |
pdf-processing |
master_supporting_docs/ |
Safe large PDF handling |
proofreading-protocol |
.tex, .qmd, quality_reports/ |
Propose-first, then apply with approval |
no-pause-beamer |
.tex |
No overlay commands in Beamer |
replication-protocol |
*.R |
Replicate original results before extending |
knowledge-base-template |
.tex, .qmd, *.R |
Notation/application registry template |
orchestrator-research |
*.R, explorations/ |
Simple orchestrator for research (no multi-round reviews) |
exploration-folder-protocol |
explorations/ |
Structured sandbox for experimental work |
exploration-fast-track |
explorations/ |
Lightweight exploration workflow (60/100 threshold) |
Templates (templates/) — reference formats for session logs, quality reports, and exploration READMEs. Not auto-loaded.
| Tool | Required For | Install |
|---|---|---|
| Claude Code | Everything | npm install -g @anthropic-ai/claude-code |
| XeLaTeX | LaTeX compilation | TeX Live or MacTeX |
| Quarto | Web slides | quarto.org/docs/get-started |
| R | Figures & analysis | r-project.org |
| pdf2svg | TikZ to SVG | brew install pdf2svg (macOS) |
| gh CLI | PR workflow | brew install gh (macOS) |
Not all tools are needed — install only what your project uses. Claude Code is the only hard requirement.
- Fill in the knowledge base (
.claude/rules/knowledge-base-template.md) with your notation, applications, and design principles - Customize the domain reviewer (
.claude/agents/domain-reviewer.md) with review lenses specific to your field - Update the color palette in your Quarto theme SCSS file — change the color variables at the top
- Add field-specific R pitfalls to
.claude/rules/r-code-conventions.md - Fill in the lecture mapping in
.claude/rules/beamer-quarto-sync.md - Customize the workflow quick reference (
.claude/WORKFLOW_QUICK_REF.md) with your non-negotiables and preferences - Set up the exploration folder (
explorations/) for experimental work
- Claude Code Documentation
- Writing a Good CLAUDE.md — official guidance on project memory
This infrastructure was extracted from Econ 730: Causal Panel Data at Emory University, developed by Pedro Sant'Anna using Claude Code over 6+ sessions. The course produced 6 complete PhD lecture decks with 800+ slides, interactive Quarto versions with plotly charts, and full R replication packages — all managed through this multi-agent workflow.
MIT License. Use freely for teaching, research, or any academic purpose.