Academic Research Skills for Claude Code

繁體中文版

A comprehensive suite of Claude Code skills for academic research, covering the full pipeline from research to publication.

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Features

• Deep Research — 13-agent research team with Socratic guided mode + systematic review / PRISMA
• Academic Paper — 12-agent paper writing with LaTeX output hardening, visualization, revision coaching, and citation conversion
• Academic Paper Reviewer — Multi-perspective peer review with 0-100 quality rubrics (EIC + 3 dynamic reviewers + Devil's Advocate)
• Academic Pipeline — Full 10-stage pipeline orchestrator with adaptive checkpoints, claim verification, and material passport

Full Pipeline

Research → Write → Integrity Check → Review (5-person) → Socratic Coaching
  → Revise → Re-Review → Re-Revise → Final Integrity Check → Finalize
  → Process Summary (with Collaboration Quality Evaluation)

Key Features:

1. Adaptive checkpoints (FULL / SLIM / MANDATORY) after every stage
2. Pre-review integrity verification — 100% reference, data, and claim validation (Phase A-E)
3. Two-stage review with Devil's Advocate + 0-100 quality rubrics
4. Socratic revision coaching between review and revision stages
5. Final integrity verification before publication
6. Output: MD + DOCX + LaTeX (APA 7.0 apa7 class / IEEE / Chicago) → PDF via tectonic
7. Post-pipeline process summary with 6-dimension collaboration quality scoring (1–100)
8. Material passport for mid-entry provenance tracking
9. Cross-skill mode advisor (14 scenarios + user archetypes)

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Showcase: Real Pipeline Output

See the complete artifacts from a real 10-stage pipeline run — including peer review reports, integrity verification reports, and the final paper:

Browse all pipeline artifacts →

Artifact	Description
Final Paper (EN)	APA 7.0 formatted, LaTeX-compiled
Final Paper (ZH)	Chinese version, APA 7.0
Integrity Report — Pre-Review	Stage 2.5: caught 15 fabricated refs + 3 statistical errors
Integrity Report — Final	Stage 4.5: zero regressions confirmed
Peer Review Round 1	EIC + 3 Reviewers + Devil's Advocate
Re-Review	Verification after revisions
Peer Review Round 2	Follow-up review
Response to Reviewers	Point-by-point author response
Post-Publication Audit Report	Independent full-reference audit: found 21/68 issues missed by 3 rounds of integrity checks

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Performance Notes

Recommended model: Claude Opus 4.6 with Max plan (or equivalent extended-thinking configuration).

The full academic pipeline (10 stages) consumes a large amount of tokens — a single end-to-end run can exceed 200K input + 100K output tokens depending on paper length and revision rounds. Budget accordingly.

Individual skills (e.g., deep-research alone, or academic-paper-reviewer alone) consume significantly less.

Recommended Settings

For the best experience with these skills, enable the following Claude Code features:

Setting	What it does	How to enable	Docs
Agent Team	Spawns subagents for parallel research, writing, and review — critical for multi-agent pipelines	Set CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1 (research preview)	Agent Teams
Ralph Loop	Keeps the session alive during long-running pipeline stages so Claude can work autonomously without timing out	Use /ralph-loop to activate	Ralph Loop
Skip Permissions	Bypasses per-tool confirmation prompts, enabling uninterrupted autonomous execution across all pipeline stages	Launch with claude --dangerously-skip-permissions	Permissions · Advanced Usage

⚠️ Skip Permissions: This flag disables all tool-use confirmation dialogs. Use at your own discretion — it is convenient for trusted, long-running pipelines but removes the safety net of manual approval. Only enable this in environments where you are comfortable with Claude executing file reads, writes, and shell commands without asking first.

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Prerequisites

Install Claude Code

Recommended: Native installer (no Node.js required, auto-updates):

# macOS / Linux
curl -fsSL https://claude.ai/install.sh | bash

# Windows (PowerShell)
irm https://claude.ai/install.ps1 | iex

Alternative: npm install (deprecated)

Requires Node.js 18+.

npm install -g @anthropic-ai/claude-code

Set Up API Key

You need an Anthropic API key. Get one at https://console.anthropic.com/

# Claude Code will prompt for your API key on first run
claude

Or set it as an environment variable:

export ANTHROPIC_API_KEY=sk-ant-xxxxx

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Installation

Method 1: As Project Skills (Recommended)

Clone this repo into your project's .claude/skills/ directory:

# Navigate to your project root
cd /path/to/your/project

# Create skills directory if it doesn't exist
mkdir -p .claude/skills

# Clone the skills
git clone https://github.com/Imbad0202/academic-research-skills.git .claude/skills/academic-research-skills

Then copy the .claude/CLAUDE.md content into your project's .claude/CLAUDE.md (merge with existing if you have one).

Global installation: To make skills available across all your projects, install to ~/.claude/skills/ instead:

mkdir -p ~/.claude/skills
git clone https://github.com/Imbad0202/academic-research-skills.git ~/.claude/skills/academic-research-skills

Method 2: As a Standalone Project

# Clone the repo
git clone https://github.com/Imbad0202/academic-research-skills.git

# Navigate to the project
cd academic-research-skills

# Start Claude Code
claude

Don't have Git? Download as ZIP instead

1. Go to https://github.com/Imbad0202/academic-research-skills
2. Click the green Code button → Download ZIP
3. Extract the ZIP to your desired location
4. For Method 1: move the extracted folder to .claude/skills/academic-research-skills inside your project
5. For standalone use: open a terminal in the extracted folder and run claude

Method 3: Claude Cowork (Desktop)

Use these skills in Claude Cowork — Claude Desktop's agentic workspace for knowledge work.

Option A: Folder Access (Quickest)

1. Clone this repo to a local folder:

   git clone https://github.com/Imbad0202/academic-research-skills.git ~/academic-research-skills

2. Open Claude Desktop → click Cowork tab (top bar)
3. Select the cloned academic-research-skills folder as the working directory
4. Claude will auto-detect the skills from SKILL.md files and load them as needed

Option B: As Project Skills

If you already have a project folder in Cowork:

cd /path/to/your/project
mkdir -p .claude/skills
git clone https://github.com/Imbad0202/academic-research-skills.git .claude/skills/academic-research-skills

Skills will auto-load when relevant to your conversation — e.g., saying "help me write a paper" triggers academic-paper.

Requirements:

• Claude Desktop (latest version) with Cowork enabled
• Paid plan (Pro, Max, Team, or Enterprise)

Method 4: Upload to claude.ai

You can load these skills via claude.ai's Project feature without installing Claude Code.

Steps:

1. Download all 4 SKILL.md files from this repo:

   • deep-research/SKILL.md
   • academic-paper/SKILL.md
   • academic-paper-reviewer/SKILL.md
   • academic-pipeline/SKILL.md

2. Sign in to claude.ai

3. Create a new Project:

   • Click Projects → Create Project in the sidebar
   • Name it "Academic Research" (or any name you prefer)

4. Upload SKILL.md files:

   • Open the Project → click Project Knowledge (right panel)
   • Click Add Content → Upload Files
   • Upload all 4 SKILL.md files

5. (Optional) Upload reference and template files for better results:

   • Files under deep-research/references/ (APA guide, methodology templates, etc.)
   • Files under academic-paper/references/ (citation formats, writing style, etc.)
   • Files under academic-paper/templates/ (paper structure templates)

6. Start chatting: Open a new conversation in the Project and say "Guide my research on X" or "Help me write a paper"

claude.ai Limitations:

• Project Knowledge file size limit: 200KB per file
• version and last_updated in SKILL.md YAML frontmatter must be under metadata:, otherwise upload will fail
• claude.ai does not support parallel multi-agent execution; results may not be as comprehensive as Claude Code
• Recommended: upload at least 4 SKILL.md files + core references for best results

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Usage

Quick Start

# Start a full research pipeline
You: "I want to write a research paper on AI's impact on higher education QA"

# Start with Socratic guidance
You: "Guide my research on AI in educational evaluation"

# Write a paper with guided planning
You: "Guide me through writing a paper on demographic decline"

# Review an existing paper
You: "Review this paper" (then provide the paper)

# Check pipeline status
You: "status"

Individual Skills

Deep Research (7 modes)

"Research the impact of AI on higher education"       → full mode
"Give me a quick brief on X"                          → quick mode
"Do a systematic review on X with PRISMA"             → systematic-review mode (new)
"Guide my research on X"                              → socratic mode (guided)
"Fact-check these claims"                             → fact-check mode
"Do a literature review on X"                         → lit-review mode
"Review this paper's research quality"                → review mode

Academic Paper (9 modes)

"Write a paper on X"                                  → full mode
"Guide me through writing a paper"                    → plan mode (guided)
"I have a draft, here are reviewer comments"          → revision mode
"Parse these reviewer comments into a roadmap"        → revision-coach mode (new)
"Convert to LaTeX" / "Convert citations to IEEE"      → format-convert mode
"Check citations"                                     → citation-check mode
"Write a bilingual abstract"                          → bilingual-abstract mode
"Polish my writing style"                             → writing-polish mode
"Write the full paper autonomously"                   → full-auto mode

Academic Paper Reviewer (5 modes)

"Review this paper"                                   → full mode (EIC + R1/R2/R3 + Devil's Advocate)
"Quick assessment of this paper"                      → quick mode
"Guide me to improve this paper"                      → guided mode
"Check the methodology"                               → methodology-focus mode
"Verify the revisions"                                → re-review mode

Academic Pipeline (Orchestrator)

"I want to write a complete research paper"           → full pipeline from Stage 1
"I already have a paper, review it"                   → mid-entry at Stage 2.5 (integrity first)
"I received reviewer comments"                        → mid-entry at Stage 4

Pipeline ends with Stage 6: Process Summary — auto-generates a paper creation process record with 6-dimension Collaboration Quality Evaluation (1–100 scoring).

Supported Languages

• Traditional Chinese (繁體中文) — default when user writes in Chinese
• English — default when user writes in English
• Bilingual abstracts (Chinese + English) for academic papers

Using a different language? Socratic mode (deep-research) and Plan mode (academic-paper) use intent-based activation — they detect the meaning of your request, not specific keywords. This means they work in any language without modification.

However, the general Trigger Keywords section (which determines whether the skill is activated at all) still lists English and Traditional Chinese keywords. If you find the skill isn't activating reliably in your language, you can add your language's keywords to the ### Trigger Keywords section in each SKILL.md file to improve matching confidence.

Supported Citation Formats

• APA 7.0 (default, including Chinese citation rules)
• Chicago (Notes & Author-Date)
• MLA
• IEEE
• Vancouver

Supported Paper Structures

• IMRaD (empirical research)
• Thematic Literature Review
• Theoretical Analysis
• Case Study
• Policy Brief
• Conference Paper

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Skill Details

Deep Research (v2.3)

13-agent pipeline for rigorous academic research:

Agent	Role
Research Question Agent	FINER-scored RQ formulation
Research Architect	Methodology design
Bibliography Agent	Systematic literature search
Source Verification Agent	Evidence grading, predatory journal detection
Synthesis Agent	Cross-source integration
Report Compiler	APA 7.0 report drafting
Editor-in-Chief	Q1 journal editorial review
Devil's Advocate	Assumption challenging (3 checkpoints)
Ethics Review Agent	AI disclosure, attribution integrity
Socratic Mentor	Guided research dialogue with convergence criteria
Risk of Bias Agent	RoB 2 + ROBINS-I assessment, traffic-light output
Meta-Analysis Agent	Effect sizes, heterogeneity, forest plot data, GRADE
Monitoring Agent	Post-pipeline literature monitoring alerts

Modes: full, quick, paper-review, lit-review, fact-check, socratic, systematic-review (new)

Academic Paper (v2.4)

12-agent pipeline for academic paper writing:

Agent	Role
Intake Agent	Configuration interview + handoff detection
Literature Strategist	Search strategy + annotated bibliography
Structure Architect	Paper outline + word allocation
Argument Builder	Thesis + claim-evidence chains
Draft Writer	Section-by-section writing
Citation Compliance	Multi-format citation audit + APA↔Chicago↔MLA↔IEEE↔Vancouver conversion
Abstract Bilingual	EN + Chinese abstracts
Peer Reviewer	5-dimension review (max 2 rounds)
Formatter	LaTeX/DOCX/PDF output — mandatory apa7 class, XeCJK bilingual, ragged2e justification fix, tectonic compilation
Socratic Mentor	Chapter-by-chapter guided planning with convergence criteria
Visualization Agent	9 chart types, matplotlib/ggplot2, APA 7.0 standards
Revision Coach Agent	Parses unstructured reviewer comments → Revision Roadmap

Modes: full, plan, revision, citation-check, format-convert, bilingual-abstract, writing-polish, full-auto, revision-coach (new)

Academic Paper Reviewer (v1.4)

7-agent multi-perspective review with 0-100 quality rubrics:

Agent	Role
Field Analyst	Identifies domain, configures reviewer personas
Editor-in-Chief	Journal fit, novelty, significance
Methodology Reviewer	Research design, statistics, reproducibility
Domain Reviewer	Literature coverage, theoretical framework
Perspective Reviewer	Cross-disciplinary, practical impact
Devil's Advocate Reviewer	Core thesis challenge, logical fallacy detection, strongest counter-argument
Editorial Synthesizer	Consensus analysis, revision roadmap, rubric-based scoring

Modes: full, re-review (verification), quick, methodology-focus, guided

Decision mapping: ≥80 Accept, 65-79 Minor Revision, 50-64 Major Revision, <50 Reject

Academic Pipeline (v2.6)

10-stage orchestrator with integrity verification, two-stage review, Socratic coaching, and collaboration evaluation:

Stage	Skill	Purpose
1. RESEARCH	deep-research	Clarify RQ, find literature
2. WRITE	academic-paper	Draft the paper
2.5. INTEGRITY	integrity_verification_agent	100% reference & data verification (v2.0: anti-hallucination mandate)
3. REVIEW	academic-paper-reviewer	5-person review (EIC + R1/R2/R3 + Devil's Advocate)
→	Socratic Revision Coaching	Guide user through review feedback
4. REVISE	academic-paper	Address review comments
3'. RE-REVIEW	academic-paper-reviewer	Verification review of revisions
→	Socratic Residual Coaching	Guide user through remaining issues (if Major)
4'. RE-REVISE	academic-paper	Final revision (if needed)
4.5. FINAL INTEGRITY	integrity_verification_agent	100% final verification (zero issues required)
5. FINALIZE	academic-paper	Ask format style → MD + DOCX + LaTeX → tectonic → PDF
6. PROCESS SUMMARY	pipeline	Paper creation process record + Collaboration Quality Evaluation (1–100)

Pipeline guarantees:

• Every stage requires user confirmation checkpoint
• Integrity verification (Stage 2.5 + 4.5) cannot be skipped
• Reproducible — standardized process with full audit trail
• Post-pipeline collaboration evaluation with honest, evidence-based scoring

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License

This work is licensed under CC-BY-NC 4.0.

You are free to:

• Share — copy and redistribute the material
• Adapt — remix, transform, and build upon the material

Under the following terms:

• Attribution — You must give appropriate credit
• NonCommercial — You may not use the material for commercial purposes

Attribution format:

Based on Academic Research Skills by Cheng-I Wu
https://github.com/Imbad0202/academic-research-skills

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Author

Cheng-I Wu (吳政宜)

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Changelog

v2.7 (2026-03-09) — Integrity Verification v2.0: Anti-Hallucination Overhaul

• integrity_verification_agent v2.0: Anti-Hallucination Mandate (no AI memory verification), eliminated gray-zone classifications (VERIFIED/NOT_FOUND/MISMATCH only), mandatory WebSearch audit trail for every reference, Stage 4.5 fresh independent verification, Gray-Zone Prevention Rule
• Known Hallucination Patterns: 5-type taxonomy (TF/PAC/IH/PH/SH) from GPTZero × NeurIPS 2025 study, 5 compound deception patterns, real-world case study, literature statistics
• Post-publication audit: Full WebSearch verification of all 68 references found 21 issues (31% error rate) that passed 3 rounds of integrity checks — proving the necessity of external verification
• Paper corrections: Removed 4 fabricated references, fixed 6 author errors, corrected 7 metadata errors, fixed 2 format issues

v2.6.2 (2026-03-09) — Intent-Based Mode Activation

• deep-research: Socratic mode now uses intent-based activation instead of keyword matching. Works in any language — detects meaning (e.g., "user wants guided thinking") rather than matching specific strings.
• academic-paper: Plan mode now uses intent-based activation. Detects intent signals like "user is uncertain how to start" or "user wants step-by-step guidance" in any language.
• Both modes now have a default rule: when intent is ambiguous, prefer socratic/plan over full — safer to guide first.
• Two-layer architecture: Layer 1 (skill activation) uses bilingual keywords for matching confidence; Layer 2 (mode routing) uses language-agnostic intent signals.

v2.6.1 (2026-03-09) — Bilingual Trigger Keywords

• deep-research: Added Traditional Chinese trigger keywords for general activation and Socratic mode.
• academic-paper: Added Traditional Chinese trigger keywords and Plan Mode trigger section.
• Both mode selection guides now include bilingual examples and Chinese-specific misselection scenarios.

v2.6 / v2.4 / v1.4 (2026-03-08) — 15+ Improvements

• deep-research v2.3: New systematic-review / PRISMA mode (7th); 3 new agents (risk_of_bias, meta_analysis, monitoring); PRISMA protocol/report templates; Socratic convergence criteria (4 signals + auto-end); Quick Mode Selection Guide
• academic-paper v2.4: 2 new agents (visualization, revision_coach); revision tracking template with 4 status types; citation format conversion (APA↔Chicago↔MLA↔IEEE↔Vancouver); statistical visualization standards; Socratic convergence criteria; revision recovery example; LaTeX output hardening — mandatory apa7 document class, text justification fix (ragged2e + etoolbox), table column width formula, bilingual abstract centering, standardized font stack (Times New Roman + Source Han Serif TC VF + Courier New), PDF via tectonic only
• academic-paper-reviewer v1.4: Quality rubrics with 0-100 scoring and behavioral indicators; decision mapping (≥80 Accept, 65-79 Minor, 50-64 Major, <50 Reject); Quick Mode Selection Guide
• academic-pipeline v2.6: Adaptive checkpoint system (FULL/SLIM/MANDATORY); Phase E Claim Verification in integrity checks; Material Passport for mid-entry provenance; cross-skill mode advisor (14 scenarios); team collaboration protocol; enhanced handoff schemas (9 schemas); integrity failure recovery example

v2.4 / v1.3 (2026-03-08)

• academic-pipeline v2.4: New Stage 6 PROCESS SUMMARY — auto-generates structured paper creation process record (MD → LaTeX → PDF, bilingual); mandatory final chapter: Collaboration Quality Evaluation with 6 dimensions scored 1–100 (Direction Setting, Intellectual Contribution, Quality Gatekeeping, Iteration Discipline, Delegation Efficiency, Meta-Learning), honest feedback, and improvement recommendations; pipeline expanded from 9 to 10 stages

v2.3 / v1.3 (2026-03-08)

• academic-pipeline v2.3: Stage 5 FINALIZE now prompts for formatting style (APA 7.0 / Chicago / IEEE); PDF must compile from LaTeX via tectonic (no HTML-to-PDF); APA 7.0 uses apa7 document class (man mode) with XeCJK for bilingual CJK support; font stack: Times New Roman + Source Han Serif TC VF + Courier New

v2.2 / v1.3 (2025-03-05)

• Cross-Agent Quality Alignment: unified definitions (peer-reviewed, currency rule, CRITICAL severity, source tier) across all agents
• deep-research v2.2: synthesis anti-patterns, Socratic auto-end conditions, DOI+WebSearch verification, enhanced ethics integrity check, mode transition matrix
• academic-paper v2.2: 4-level argument scoring, plagiarism screening, 2 new failure paths (F11 Desk-Reject Recovery, F12 Conference-to-Journal), Plan→Full mode conversion
• academic-paper-reviewer v1.3: DA vs R3 role boundaries, CRITICAL finding criteria, consensus classification (4/3/SPLIT/DA-CRITICAL), confidence score weighting, Asian & Regional Journals reference
• academic-pipeline v2.2: checkpoint confirmation semantics, mode switching matrix, failure fallback matrix, state ownership protocol, material version control

v2.0.1 (2026-03)

• Simplify 4 SKILL.md (-371 lines, -16.5%): remove cross-skill duplication, inline templates → file references, redundant routing tables, duplicate mode selection sections
• Fix revision loop cap contradiction between academic-paper and academic-pipeline

v2.0 (2026-02)

• academic-pipeline v2.0: 5→9 stages, mandatory integrity verification, two-stage review, Socratic revision coaching, reproducibility guarantees
• academic-paper-reviewer v1.1: +Devil's Advocate Reviewer (7th agent), +re-review mode (verification), +post-review Socratic coaching
• New agent: integrity_verification_agent — 100% reference/data verification with audit trail
• New agent: devils_advocate_reviewer_agent — 8-dimension thesis challenger
• Output order: MD + DOCX → ask LaTeX → confirm → PDF

v1.0 (2026-02)

• Initial release
• deep-research v2.0 (10 agents, 6 modes including socratic)
• academic-paper v2.0 (10 agents, 8 modes including plan)
• academic-paper-reviewer v1.0 (6 agents, 4 modes including guided)
• academic-pipeline v1.0 (orchestrator)