My Claude Code Setup

Name: Claude Code Academic Workflow
Author: Pedro H. C. Sant'Anna

Pedro H. C. Sant'Anna · Emory University

Actively developed and maintained. This summarizes how I use Claude Code for academic work — slides, papers, data analysis, and more. Adopted by 15+ research groups across economics, energy, political science, and engineering. I keep learning and updating these files.

A foundation for AI-assisted academic work using Claude Code. You describe what you want — lecture slides, a research paper, a data analysis, a replication package — and Claude plans the approach, runs specialized agents, fixes issues, verifies quality, and presents results. Like a contractor who handles the entire job.

Read the full guide

What's in the template

Full academic lifecycle — not just slides: research papers, data analysis, replication packages, proposals, and presentations
Contractor mode via skills — you describe the task; Claude picks a skill (/create-lecture, /review-paper, /qa-quarto, …) that runs the orchestrator pattern internally: plan, implement, review with agents, fix, re-verify, score against quality thresholds
Beamer → Quarto pipeline — 11-phase translation with TikZ-to-SVG and ggplot-to-plotly conversion
14 specialized agents — proofreader, slide auditor, pedagogy reviewer, R reviewer, TikZ critic, domain reviewer, adversarial QA pair, translator, verifier, claim-verifier (Chain-of-Verification), plus simulated-peer-review trio (editor, domain referee, methods referee)
Adversarial critic-fixer loop — two agents that check each other's work across up to 5 rounds — the critic can't fix, the fixer can't approve
Quality scoring with mandatory verification — every file scored 0–100; /commit halts below 80 (user can override with an explicit reason); skills that implement the orchestrator pattern verify every output before reporting done
30 slash commands + 24 context-aware rules — /compile-latex, /proofread, /deploy, /commit, /qa-quarto, /lit-review, /review-paper, /respond-to-referees, /new-diagram, /data-analysis, /audit-reproducibility, /checkpoint, /preregister, and more — plus quality gates, TikZ prevention/measurement, notation consistency, and R conventions
Simulated peer review — /review-paper --peer <journal> runs a full editorial pipeline: editor desk review, two blind referees with deliberately different dispositions (STRUCTURAL / CREDIBILITY / MEASUREMENT / POLICY / THEORY / SKEPTIC), editorial synthesis with FATAL / ADDRESSABLE / TASTE classification. Calibrated to 5 econ journals (AER / QJE / JPE / ECMA / ReStud) plus a template for adding your own field. Adapted from Hugo Sant’Anna’s clo-author with permission.
Research workflow skills — /lit-review for literature synthesis, /research-ideation for hypothesis generation, /interview-me to formalize ideas, /review-paper for manuscript review, /data-analysis for end-to-end R analysis
Smart hooks — Desktop notifications (macOS/Linux), pre-compaction context snapshots to session logs, progressive context-usage warnings, post-edit verify reminders
TikZ diagram pipeline — 8-snippet gallery (DAGs, DiD, event study, timeline, regression scatter, flowchart, supply-demand), /new-diagram scaffold with prevention pre-checks, production Beamer preamble with palette-synced Quarto theme, measurement-based collision audits via tikz-reviewer
Plan-first workflow with continuous learning — non-trivial tasks start in plan mode; [LEARN:tag] corrections persist in MEMORY.md across sessions; plans survive context compression
Research exploration workflow — structured explorations/ sandbox with fast-track prototyping (60/100 threshold), simplified orchestrator for R/research, and merge-only quality reporting
Automated session log enforcement — a lightweight Stop hook reminds Claude to keep session logs current; Beamer-Quarto sync enforced via auto-loaded rules
2026 features — effort levels for cost control, permission modes, expanded hook events, skill frontmatter (effort, context: fork), /batch for parallel refactoring, plugins, and headless CLI mode
Community ecosystem — extended by clo-author, claudeblattman, MixtapeTools, autoresearch, and ClaudeCodeTools — 15+ research groups have adopted this workflow

Getting started

# Fork this repo on GitHub, then:
git clone https://github.com/YOUR_USERNAME/claude-code-my-workflow.git my-project
cd my-project

Then start Claude Code and paste the starter prompt from the guide. Describe your project in 2–3 sentences and Claude will read all the configuration files, fill in the placeholders, and adapt the workflow to your use case.

The full guide walks through everything: setup, agents, quality gates, workflow patterns, and customization.

Read the full guide Copy the starter prompt

Source

Everything is on GitHub: pedrohcgs/claude-code-my-workflow