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.
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.
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.
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).
| 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 |
| When you say... | Skill activates |
|---|---|
| "design an ablation study" | Experiment Design |
| "find related papers on X" | Literature Research |
| "review my methods section for consistency" | Paper Verification |
| "check if my numbers match the code" | Paper Verification |
| "analyze dataset bias" | Dataset Curation |
| "prepare code for open-source release" | Research Publishing |
| "what will reviewers ask about this?" | Reviewer Defense |
| "setup latex for CVPR" | LaTeX Setup |
| 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 |
| What it catches | Real incident that inspired it |
|---|---|
| Unverified claims, wrong targets, scope creep, dropped requests, assumptions stated as facts | Claude removed introduction novelty claims, analyzed wrong data split, dropped a verification question mid-commit |
| Ambiguous short messages before costly actions | "done?" misread as "dont?", launched unwanted upload |
| Missing citation verification when editing .tex/.bib | Claude propagated unverified author names and venue info |
| LaTeX compilation errors after .tex edits | Errors compounded across multiple edits before being caught |
| Unreviewed generated images/figures | Claude analyzed metrics but never looked at the actual plots |
| Research state loss before context overflow | Long research sessions lost context, leading to rushed conclusions |
| phd-skills | flonat/claude-research | Others | |
|---|---|---|---|
| Commands to learn | 6 | 39 | 13-20 |
| Research integrity hooks | 6 (prompt + command) | 1 | 0 |
| Paper-code consistency audit | 5-dimension parallel | Read-only, no code cross-ref | None |
| Experiment monitoring + SSH notifications | Yes (ntfy/slack/email) | No | No |
| External dependencies | None | npm + pip + MCP servers | MCP required |
| Install time | 30 seconds | 10+ minutes | Varies |
- No MCP dependency — works on any machine, including SSH
- Methodology over scripts — skills teach the approach, Claude generates code for your specific setup (wandb, neptune, local files, whatever)
- Human oversight first — Claude makes premature claims and jumps to conclusions. Every skill builds in verification checkpoints
- Actionable output — ranked suggestions with specific fixes, never just a list of findings
MIT — use it, fork it, adapt it to your research.
Built with frustration and care during a PhD at METU.
