A Claude Code skill for medical/scientific paper writing. Covers the entire manuscript lifecycle from literature search to submission, peer review response, and rejection handling. 日本語版はこちら → README.ja.md
Messy notes in. Board-ready slides out. One skill for your AI agent: turn notes, metrics, and prose into consulting-grade visuals — as real SVG slides, as an animated HTML deck, or as a spec any designer or tool can execute. Python 3 standard library only.
@kgraph57FAQ
paper-writer-skill is a Claude Code plugin with 1 hand-picked skill for content work, indexed on Flowy. Install it with the command on its page. It includes paper-writer-skill. Its skills do not fire on their own yet. Request auto-invocation to have Flowy route them as you prompt. Free and open source.
$ npx -y skills add kgraph57/paper-writer-skill --agent claude-code
A Claude Code skill for medical/scientific paper writing. Covers the entire manuscript lifecycle from literature search to submission, peer review response, and rejection handling.
日本語版はこちら → README.ja.md
Not just a manuscript factory (write → format → submit) but a research engine:
a discovery loop that generates and ranks research questions, checks their novelty
against the live literature, designs and powers the study, locks a pre-registered
plan, and — after the manuscript is drafted — red-teams its own central claim before
any journal sees it. Two things stay human and protected at every gate: the 💡 IDEA
(what is worth asking, what it means, what is ethical) and the 📊 DATA (real,
IRB-approved, never machine-originated). See
references/ai-for-science-model.md.
A pipeline that generates and manages IMRAD-format project directories with structured Markdown files, a literature matrix, and quality checklists.
graph LR
P0["−1. Discovery\n(question · novelty · design · pre-reg)"] --> P1[1. Literature Search]
P1 --> P2[2. Outline]
P2 --> P25[2.5 Tables/Figures]
P25 --> P3[3. Draft]
P3 --> P4[4. Humanize]
P4 --> P5[5. References]
P5 --> P6[6. Quality Review]
P6 --> P65["6.5 Adversarial Review"]
P65 --> P7[7. Pre-Submission]
P65 -.->|KILL| P0
P7 --> P8["8. Revision ①"]
P8 --> P9["9. Post-Acceptance"]
P7 -.-> P10["10. Rejection → Resubmit"]
P10 -.-> P1
Every phase is guarded by a quality gate. If the gate returns FAIL, the system automatically generates structured feedback, dispatches a fixer agent in revision_mode, and re-checks — up to 3 iterations before escalating to the user. No phase proceeds until its gate returns PASS.
flowchart TD
subgraph "Per-Phase Loop (max 3 iterations)"
A["Phase N Complete"] --> B{"Quality Gate"}
B -->|PASS| C["→ Phase N+1"]
B -->|FAIL iter < 3| D["Generate feedback.md"]
D --> E["Fixer Agent\n(revision_mode)"]
E --> B
B -->|FAIL iter ≥ 3| F["⚠ Escalate to User"]
end
style B fill:#f9a825,stroke:#f57f17,color:#000
style C fill:#66bb6a,stroke:#388e3c,color:#fff
style F fill:#ef5350,stroke:#c62828,color:#fff
flowchart LR
subgraph "Phase 1"
G1["📚 Literature\n≥10 papers\nAll DOIs valid"]
end
subgraph "Phase 2"
G2["📋 Outline\nAll IMRAD sections\n≥2 citations mapped"]
end
subgraph "Phase 2.5"
G25["📊 Tables/Figures\nAll designs complete\nJournal limits OK"]
end
subgraph "Phase 3"
G3["✍️ Section Draft\nScore ≥80%\nMust Fix = 0"]
end
subgraph "Phase 4"
G4["🔍 Humanize\nHigh-priority\nAI patterns = 0"]
end
subgraph "Phase 5"
G5["📖 References\nFabrication = 0\nOrphan cites = 0"]
end
subgraph "Phase 6"
G6["🔗 Cross-Section\nPASS or\nCONDITIONAL_PASS"]
end
subgraph "Phase 7"
G7["📦 Submission\nAll docs ready\nWord count OK"]
end
G1 --> G2 --> G25 --> G3 --> G4 --> G5 --> G6 --> G7
Phases are parallelized with specialized agents running concurrently:
flowchart TB
subgraph P1["Phase 1 — Literature Search (3 parallel)"]
L1[PubMed Searcher]
L2[Google Scholar Searcher]
L3[Domain DB Searcher]
end
subgraph P3["Phase 3 — Drafting (grouped parallel)"]
direction LR
D1[Methods] --> D3[Intro]
D2[Results] --> D4[Conclusion]
end
subgraph P4["Phase 4 — Humanize (up to 6 parallel)"]
H1[Humanizer × N sections]
end
subgraph P6["Phase 6 — Quality Review"]
R1[Section Reviewer ×N]
R2[Quality Gate — opus]
end
L1 & L2 & L3 --> MERGE["Merge Matrix"]
MERGE --> D1 & D2
D3 & D4 --> H1
H1 --> R1
R1 --> R2
| Agent | Role | Model |
|---|---|---|
paper-lit-searcher | Database-specific literature search | sonnet |
paper-table-figure-planner | Table and figure design | sonnet |
paper-section-drafter | Section drafting (parameterized) | sonnet |
paper-humanizer | AI writing pattern removal | haiku |
paper-ref-builder | Citation collection and verification | sonnet |
paper-section-reviewer | Per-section quality check | sonnet |
paper-quality-gate | Cross-section consistency + final verdict | opus |
| Type | Structure | Reporting Guideline |
|---|---|---|
| Original Article | Full IMRAD | STROBE / CONSORT |
| Case Report | Intro / Case / Discussion | CARE |
| Review Article | Thematic sections | — |
| Systematic Review | PRISMA-compliant | PRISMA 2020 |
| Letter / Short Communication | Condensed IMRAD | Same as original |
| Study Protocol | SPIRIT-compliant | SPIRIT 2025 |
/paper-writer
Or use natural language triggers:
write paper / start manuscript / research paper論文を書く / 論文執筆 / 原稿作成The skill prompts you for:
When a target journal is specified, the skill automatically looks up word limits, citation style, abstract format, and other requirements.
Each paper project generates a comprehensive directory for managing the entire research lifecycle:
{project-dir}/
├── README.md # Project dashboard (status, timeline, links)
├── 00_literature/ # Literature search & matrix
├── 01_outline.md # Paper skeleton
├── sections/ # Manuscript sections (writing order)
│ ├── 02_methods.md ... 08_title.md
├── tables/ # Tables (numbered)
├── figures/ # Figures + captions
├── supplements/ # Supplementary materials
│ ├── supplementary-tables/
│ ├── supplementary-figures/
│ └── appendices/
├── data/ # Research data (raw → processed → analysis)
│ ├── raw/ # Original data (READ-ONLY, gitignored)
│ ├── processed/ # Cleaned, de-identified
│ ├── analysis/ # Statistical output
│ └── data-dictionary.md
├── ethics/ # IRB, consent, protocol, registration
├── submissions/ # Submission history (v1_bmj/, v2_lancet/, ...)
│ └── v1_{journal}/ # Compiled manuscript + cover letter + declarations
├── revisions/ # Revision rounds (r1/, r2/, ...)
│ └── r1/ # Reviewer comments + response + diff
├── coauthor-review/ # Co-author feedback tracking
├── correspondence/ # Editor & reviewer communication log
├── references/ # Formatted reference list
├── checklists/ # Quality gates, reporting guideline tracking
└── log/ # Decisions, meetings, timeline
paper-writer/
├── SKILL.md # Main workflow definition
├── CHANGELOG.md # Version history
├── README.md # This file
├── README.ja.md # Japanese documentation
├── requirements.txt # Python dependencies for utility scripts
│
├── templates/ # 37 files — Section templates
│ ├── project-init.md # Project initialization (Original Article)
│ ├── project-init-case.md # Project initialization (Case Report)
│ ├── research-question.md # Question forge and FINER scoring
│ ├── study-design.md # Study design, variables, power, feasibility
│ ├── preregistration.md # Pre-registration lock template
│ ├── human-loop-ledger.md # Human/AI accountability ledger
│ ├── literature-matrix.md # Literature comparison matrix
│ ├── methods.md # Methods writing guide
│ ├── results.md # Results writing guide
│ ├── introduction.md # Introduction writing guide
│ ├── discussion.md # Discussion writing guide
│ ├── conclusion.md # Conclusion writing guide
│ ├── abstract.md # Abstract writing guide (Original Article)
│ ├── cover-letter.md # Cover letter template
│ ├── submission-ready.md # Pre-submission checklist
│ ├── case-report.md # Case presentation (CARE-compliant)
│ ├── case-introduction.md # Case report introduction
│ ├── case-abstract.md # Case report abstract (CARE format)
│ ├── review-article.md # Review article structure guide
│ ├── sr-outline.md # Systematic review outline
│ ├── sr-data-extraction.md # SR data extraction template
│ ├── sr-prisma-flow.md # PRISMA flow diagram
│ ├── sr-grade.md # GRADE evidence assessment
│ ├── sr-rob.md # Risk of bias assessment
│ ├── sr-prospero.md # PROSPERO registration template
│ ├── sr-screening-pipeline.md # Dual-screening execution pipeline
│ ├── response-to-reviewers.md # Response to reviewers template
│ ├── revision-cover-letter.md # Revision cover letter
│ ├── declarations.md # Declarations (ethics, COI, funding, AI disclosure)
│ ├── graphical-abstract.md # Graphical abstract guide
│ ├── title-page.md # Title page template
│ ├── highlights.md # Key points / highlights (JAMA, BMJ, etc.)
│ ├── limitations-guide.md # Limitations section guide
│ ├── acknowledgments.md # Acknowledgments template
│ ├── proof-correction.md # Post-acceptance proof correction guide
│ ├── data-management.md # Data management (raw/processed/analysis)
│ └── analysis-workflow.md # Data analysis workflow guide
│
├── references/ # 30 files — Reference materials
│ ├── ai-for-science-model.md # Research-engine operating model
│ ├── novelty-check.md # Live-literature novelty check
│ ├── adversarial-review.md # Design/manuscript red-team review
│ ├── imrad-guide.md # IMRAD structure and writing principles
│ ├── section-checklist.md # Per-section quality checklist
│ ├── citation-guide.md # Citation formatting and management
│ ├── citation-verification.md # Citation verification guide
│ ├── reporting-guidelines.md # Reporting guidelines summary
│ ├── reporting-guidelines-full.md # 20+ reporting guidelines with checklists
│ ├── humanizer-academic.md # AI writing detection (EN 18 + JP 13 patterns)
│ ├── statistical-reporting.md # Statistical reporting guide
│ ├── statistical-reporting-full.md # Extended SAMPL guide
│ ├── journal-selection.md # Journal selection strategy
│ ├── pubmed-query-builder.md # PubMed search query builder
│ ├── multilingual-guide.md # Multilingual support guide
│ ├── coauthor-review.md # Co-author review process
│ ├── ai-disclosure.md # ICMJE 2023 AI disclosure guide
│ ├── tables-figures-guide.md # Tables and figures creation guide
│ ├── keywords-guide.md # Keywords and MeSH selection strategy
│ ├── supplementary-materials.md # Supplementary materials strategy
│ ├── hook-compatibility.md # Claude Code hook compatibility
│ ├── submission-portals.md # Submission portal guide
│ ├── open-access-guide.md # OA models, APCs, CC licenses
│ ├── clinical-trial-registration.md # Clinical trial registration guide
│ ├── abstract-formats.md # Journal-specific abstract formats
│ ├── word-count-limits.md # Word count limits by journal
│ ├── coi-detailed.md # COI categories, CRediT taxonomy, ORCID
│ ├── desk-rejection-prevention.md # Desk rejection prevention
│ ├── journal-reformatting.md # Journal reformatting and cascading strategy
│ └── master-reference-list.md # Master URL list (100+ links, 13 categories)
│
├── scripts/ # 8 files — Utilities & Analysis
│ ├── compile-manuscript.sh # Compile sections into single manuscript
│ ├── word-count.sh # Word count utility
│ ├── forest-plot.py # Forest plot generator
│ ├── sr-dedup.py # SR record parsing and de-duplication
│ ├── sr-pdf-link.py # Link full-text PDFs to records by DOI
│ ├── sr-prisma-count.py # PRISMA flow counts and consistency checks
│ ├── table1.py # Table 1 generator (baseline characteristics)
│ └── analysis-template.py # Statistical analysis template (t-test, logistic, survival)
│
├── tests/
│ └── test_scripts.py # Regression tests for utility scripts
│
└── .github/workflows/
└── tests.yml # CI: syntax checks + regression tests
Total: 83 tracked files (37 templates + 30 references + 8 scripts + tests + CI + root docs/config)
| Phase | Description | Key Operations |
|---|---|---|
| 0 | Project Initialization | Journal requirements lookup, reporting guideline selection, directory generation, data management & analysis |
| 1 | Literature Search | PubMed/Google Scholar search, literature matrix creation |
| 2 | Outline | Paper skeleton design (user approval required) |
| 2.5 | Tables & Figures | Design tables/figures before writing prose |
| 3 | Drafting | Methods → Results → Intro P3 + Conclusion → Discussion → Intro P1-2 → Abstract → Title |
| 4 | Humanize | AI writing pattern removal (EN 18 + JP 13 patterns) |
| 5 | References | Citation formatting, deduplication, existence verification |
| 6 | Quality Review | Cross-section verification, reporting guideline compliance |
| 7 | Pre-Submission | Cover letter, title page, declarations, final checklist |
| 8 | Revision | Reviewer comment organization, response letter, revision implementation |
| 9 | Post-Acceptance | Proof review (24-72 hr), correction submission, post-publication tasks |
| 10 | Rejection & Resubmission | Assessment, quick reformat, cascading submission strategy |
CONSORT 2025, STROBE, PRISMA 2020, CARE, STARD 2015, SQUIRE 2.0, SPIRIT 2025, TRIPOD+AI 2024, ARRIVE 2.0, CHEERS 2022, MOOSE, TREND, SRQR, COREQ, AGREE II, RECORD, STREGA, ENTREQ, PRISMA-ScR, GRADE
| Language | Coverage |
|---|---|
| English | All templates and guides, 18 AI writing detection patterns |
| Japanese | All templates bilingual (EN/JP), 13 AI writing detection patterns, である-style |
A dedicated phase (Phase 4) to remove AI-generated writing patterns from academic manuscripts.
references/master-reference-list.md contains 100+ URLs organized in 13 categories:
Clone this repository into the Claude Code skills directory:
git clone https://github.com/kgraph57/paper-writer-skill.git ~/.claude/skills/paper-writer
Register the skill in Claude Code settings:
// Add to "skills" in ~/.claude/settings.json
{
"skills": {
"paper-writer": {
"path": "~/.claude/skills/paper-writer"
}
}
}
python -m pip install -r requirements.txtpython -m py_compile scripts/*.py
bash -n scripts/*.sh
python -m unittest discover -s tests -v
Private repository.
See CHANGELOG.md for details.
.github/
workflows/
tests.yml
.gitignore
CHANGELOG.md
README.ja.md
README.md
references/
abstract-formats.md
adversarial-review.md
ai-disclosure.md
ai-for-science-model.md
citation-guide.md
citation-verification.md
clinical-trial-registration.md
coauthor-review.md
coi-detailed.md
desk-rejection-prevention.md
hook-compatibility.md
humanizer-academic.md
imrad-guide.md
journal-reformatting.md
journal-selection.md
keywords-guide.md
master-reference-list.md
multilingual-guide.md
novelty-check.md
open-access-guide.md
pubmed-query-builder.md
reporting-guidelines-full.md
reporting-guidelines.md
section-checklist.md
statistical-reporting-full.md
statistical-reporting.md
submission-portals.md
supplementary-materials.md
tables-figures-guide.md
word-count-limits.md
requirements.txt
scripts/
analysis-template.py
compile-manuscript.sh
forest-plot.py
sr-dedup.py
sr-pdf-link.py
sr-prisma-count.py
table1.py
word-count.sh
SKILL.md
templates/
abstract.md
acknowledgments.md
analysis-workflow.md
case-abstract.md
case-introduction.md
case-report.md
conclusion.md
cover-letter.md
data-management.md
declarations.md
discussion.md
graphical-abstract.md
highlights.md
human-loop-ledger.md
introduction.md
limitations-guide.md
literature-matrix.md
methods.md
preregistration.md
project-init-case.md
project-init.md
proof-correction.md
research-question.md
response-to-reviewers.md
results.md
review-article.md
revision-cover-letter.md
sr-data-extraction.md
sr-grade.md
sr-outline.md
sr-prisma-flow.md
sr-prospero.md
sr-rob.md
sr-screening-pipeline.md
study-design.md
submission-ready.md
title-page.md
tests/
test_scripts.py© 2026 Flowy · Free and open source
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