Research integrity plugin for Claude Code — paper auditing, citation verification, experiment analysis, and methodology-first skills for academic workflows.
# Add to your Claude Code skills
git clone https://github.com/fcakyon/phd-skills
README.md
phd-skills
Research integrity plugin for Claude Code — paper auditing, citation
verification, experiment analysis, and methodology-first skills for
academic workflows.
Built by Fatih Cagatay Akyon
(1300+ citations, 7 patents) after 200+ Claude Code sessions, tens of
critical AI mistakes caught the hard way, and thousands of hours of
PhD research. Every guardrail in this plugin traces to a real mistake.
Why This Plugin Exists
I use Claude Code daily for my PhD. It's powerful, but it
makes research-specific mistakes that cost hours:
It typed "done?" as "dont?" and launched an unwanted upload of thousands of files
It analyzed my full dataset when I asked for a specific 4k/2k/2k split
It claimed a test covered a bug it had never actually verified
It never once looked at a figure it generated — just trusted the numbers
Other plugins give you more commands. This plugin gives you guardrails.
Install
claude plugin marketplace add fcakyon/phd-skills
claude plugin install phd-skills@phd-skills
Then run /phd-skills:setup inside Claude Code to configure notifications, LaTeX, and allowlist.
Usage
Open Claude Code in your paper directory, then:
/phd-skills:xray — audit paper against code and data across 5 dimensions, get prioritized fixes
/phd-skills:factcheck — verify all BibTeX entries and cited claims against DBLP
/phd-skills:fortify CVPR — anticipate reviewer questions, rank ablations, and suggest paper improvements
/phd-skills:gaps neural architecture search — find what's missing in the literature
/loop 30m check experiment logs, notify me if metrics beat the baseline or if loss starts to diverge
"check if my numbers match the code" — skills auto-trigger, no slash command needed
"make code publish ready" — prepares code for open-source release with license, docs, and reproducibility checks
After running /phd-skills:setup, all Claude Code notifications (task completion,
background agents) are forwarded to your configured service (ntfy/Slack/email).
What You Get
Commands
| Command | What it does |
|---------|-------------|
| /phd-skills:xray | Audit paper against code and data (5 parallel dimensions) |
| /phd-skills:factcheck | Verify BibTeX entries and cited claims against DBLP |
| /phd-skills:gaps <topic> | Literature gap analysis with web confirmation |
| /phd-skills:fortify [venue] | Select strongest ablations + anticipate reviewer questions |
| /phd-skills:setup | Interactive onboarding (notifications, allowlist, LaTeX) |
| /phd-skills:help | Show all features at a glance |
Skills (auto-trigger — just describe what you need)
| Agent | What it does | Special |
|-------|-------------|---------|
| paper-auditor | Cross-checks paper claims vs code and data | Runs in isolated worktree, remembers patterns across sessions |
| experiment-analyzer | Analyzes results from wandb/neptune/local/any format | Can schedule monitoring via cron, sends SSH notifications |
Research Guardrails (run silently — you never invoke these)
The agent harness performance optimization system. Skills, instincts, memory, security, and research-first development for Claude Code, Codex, Opencode, Cursor and beyond.
