Download skills/04-K-Dense-AI-claude-scientific-writer/peer-review/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does peer-review live?
The publisher keeps it at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.
Which agents can use peer-review?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.
Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.
name: peer-review
description: "Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines."
allowed-tools: [Read, Write, Edit, Bash]
Scientific Critical Evaluation and Peer Review
Overview
Peer review is a systematic process for evaluating scientific manuscripts. Assess methodology, statistics, design, reproducibility, ethics, and reporting standards. Apply this skill for manuscript and grant review across disciplines with constructive, rigorous evaluation.
When to Use This Skill
This skill should be used when:
Conducting peer review of scientific manuscripts for journals
Evaluating grant proposals and research applications
Assessing methodology and experimental design rigor
Reviewing statistical analyses and reporting standards
Evaluating reproducibility and data availability
Checking compliance with reporting guidelines (CONSORT, STROBE, PRISMA)
Providing constructive feedback on scientific writing
Related Resource: The venue-templates skill provides reviewer_expectations.md with detailed guidance on what reviewers look for at different venues (Nature/Science, Cell Press, medical journals, ML conferences). Use this to calibrate your review standards to the target venue.
Visual Enhancement with Scientific Schematics
When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.
If your document does not already contain schematics or diagrams:
Use the scientific-schematics skill to generate AI-powered publication-quality diagrams
Simply describe your desired diagram in natural language
Nano Banana Pro will automatically generate, review, and refine the schematic
For new documents: Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.
Objectivity: Are results presented without over-interpretation?
Completeness: Are all relevant results included, including negative results?
Reproducibility: Are raw data or summary statistics provided?
Common issues to identify:
Selective reporting of results
Inappropriate statistical tests
Missing error bars or measures of variability
Over-fitting or circular analysis
Batch effects or confounding variables
Missing controls or validation experiments
Discussion
Interpretation: Are conclusions supported by the data?
Limitations: Are study limitations acknowledged and discussed?
Context: Are findings placed appropriately within existing literature?
Speculation: Is speculation clearly distinguished from data-supported conclusions?
Significance: Are implications and importance clearly articulated?
Future directions: Are next steps or unanswered questions discussed?
Red flags:
Overstated conclusions
Ignoring contradictory evidence
Causal claims from correlational data
Inadequate discussion of limitations
Mechanistic claims without mechanistic evidence
References
Completeness: Are key relevant papers cited?
Currency: Are recent important studies included?
Balance: Are contrary viewpoints appropriately cited?
Accuracy: Are citations accurate and appropriate?
Self-citation: Is there excessive or inappropriate self-citation?
Stage 3: Methodological and Statistical Rigor
Evaluate the technical quality and rigor of the research with particular attention to common pitfalls.
Statistical Assessment:
Are statistical assumptions met (normality, independence, homoscedasticity)?
Are effect sizes reported alongside p-values?
Is multiple testing correction applied appropriately?
Are confidence intervals provided?
Is sample size justified with power analysis?
Are parametric vs. non-parametric tests chosen appropriately?
Are missing data handled properly?
Are exploratory vs. confirmatory analyses distinguished?
Experimental Design:
Are controls appropriate and adequate?
Is replication sufficient (biological and technical)?
Are potential confounders identified and controlled?
Is randomization properly implemented?
Are blinding procedures adequate?
Is the experimental design optimal for the research question?
Computational/Bioinformatics:
Are computational methods clearly described and justified?
Are software versions and parameters documented?
Is code made available for reproducibility?
Are algorithms and models validated appropriately?
Are assumptions of computational methods met?
Is batch correction applied appropriately?
Stage 4: Reproducibility and Transparency
Assess whether the research meets modern standards for reproducibility and open science.
Data Availability:
Are raw data deposited in appropriate repositories?
Are accession numbers provided for public databases?
Are data sharing restrictions justified (e.g., patient privacy)?
Are data formats standard and accessible?
Code and Materials:
Is analysis code made available (GitHub, Zenodo, etc.)?
Are unique materials available or described sufficiently for recreation?
Are protocols detailed in sufficient depth?
Reporting Standards:
Does the manuscript follow discipline-specific reporting guidelines (CONSORT, PRISMA, ARRIVE, MIAME, MINSEQE, etc.)?
See references/reporting_standards.md for common guidelines
Are all elements of the appropriate checklist addressed?
Stage 5: Figure and Data Presentation
Evaluate the quality, clarity, and integrity of data visualization.
Quality Checks:
Are figures high resolution and clearly labeled?
Are axes properly labeled with units?
Are error bars defined (SD, SEM, CI)?
Are statistical significance indicators explained?
Are color schemes appropriate and accessible (colorblind-friendly)?
Are scale bars included for images?
Is data visualization appropriate for the data type?
Integrity Checks:
Are there signs of image manipulation (duplications, splicing)?
Are Western blots and gels appropriately presented?
Are representative images truly representative?
Are all conditions shown (no selective presentation)?
Clarity:
Can figures stand alone with their legends?
Is the message of each figure immediately clear?
Are there redundant figures or panels?
Would data be better presented as tables or figures?
Stage 6: Ethical Considerations
Verify that the research meets ethical standards and guidelines.
Human Subjects:
Is IRB/ethics approval documented?
Is informed consent described?
Are vulnerable populations appropriately protected?
Is patient privacy adequately protected?
Are potential conflicts of interest disclosed?
Animal Research:
Is IACUC or equivalent approval documented?
Are procedures humane and justified?
Are the 3Rs (replacement, reduction, refinement) considered?
Are euthanasia methods appropriate?
Research Integrity:
Are there concerns about data fabrication or falsification?
Is authorship appropriate and justified?
Are competing interests disclosed?
Is funding source disclosed?
Are there concerns about plagiarism or duplicate publication?
Stage 7: Writing Quality and Clarity
Assess the manuscript's clarity, organization, and accessibility.
Structure and Organization:
Is the manuscript logically organized?
Do sections flow coherently?
Are transitions between ideas clear?
Is the narrative compelling and clear?
Writing Quality:
Is the language clear, precise, and concise?
Are jargon and acronyms minimized and defined?
Is grammar and spelling correct?
Are sentences unnecessarily complex?
Is the passive voice overused?
Accessibility:
Can a non-specialist understand the main findings?
Are technical terms explained?
Is the significance clear to a broad audience?
Structuring Peer Review Reports
Organize feedback in a hierarchical structure that prioritizes issues and provides actionable guidance.
Summary Statement
Provide a concise overall assessment (1-2 paragraphs):
Brief synopsis of the research
Overall recommendation (accept, minor revisions, major revisions, reject)
Key strengths (2-3 bullet points)
Key weaknesses (2-3 bullet points)
Bottom-line assessment of significance and soundness
Major Comments
List critical issues that significantly impact the manuscript's validity, interpretability, or significance. Number these sequentially for easy reference.
Major comments typically include:
Fundamental methodological flaws
Inappropriate statistical analyses
Unsupported or overstated conclusions
Missing critical controls or experiments
Serious reproducibility concerns
Major gaps in literature coverage
Ethical concerns
For each major comment:
Clearly state the issue
Explain why it's problematic
Suggest specific solutions or additional experiments
Indicate if addressing it is essential for publication
Minor Comments
List less critical issues that would improve clarity, completeness, or presentation. Number these sequentially.
Minor comments typically include:
Unclear figure labels or legends
Missing methodological details
Typographical or grammatical errors
Suggestions for improved data presentation
Minor statistical reporting issues
Supplementary analyses that would strengthen conclusions
Requests for clarification
For each minor comment:
Identify the specific location (section, paragraph, figure)
State the issue clearly
Suggest how to address it
Specific Line-by-Line Comments (Optional)
For manuscripts requiring detailed feedback, provide section-specific or line-by-line comments:
Reference specific page/line numbers or sections
Note factual errors, unclear statements, or missing citations
Suggest specific edits for clarity
Questions for Authors
List specific questions that need clarification:
Methodological details that are unclear
Seemingly contradictory results
Missing information needed to evaluate the work
Requests for additional data or analyses
Tone and Approach
Maintain a constructive, professional, and collegial tone throughout the review.
Best Practices:
Be constructive: Frame criticism as opportunities for improvement
Be specific: Provide concrete examples and actionable suggestions
Be balanced: Acknowledge strengths as well as weaknesses
Be respectful: Remember that authors have invested significant effort
Be objective: Focus on the science, not the scientists
Be thorough: Don't overlook issues, but prioritize appropriately
Be clear: Avoid ambiguous or vague criticism
Avoid:
Personal attacks or dismissive language
Sarcasm or condescension
Vague criticism without specific examples
Requesting unnecessary experiments beyond the scope
Demanding adherence to personal preferences vs. best practices
Revealing your identity if reviewing is double-blind
Special Considerations by Manuscript Type
Original Research Articles
Emphasize rigor, reproducibility, and novelty
Assess significance and impact
Verify that conclusions are data-driven
Check for complete methods and appropriate controls
Reviews and Meta-Analyses
Evaluate comprehensiveness of literature coverage
Assess search strategy and inclusion/exclusion criteria
Verify systematic approach and lack of bias
Check for critical analysis vs. mere summarization
For meta-analyses, evaluate statistical approach and heterogeneity
Methods Papers
Emphasize validation and comparison to existing methods
Assess reproducibility and availability of protocols/code
Evaluate improvements over existing approaches
Check for sufficient detail for implementation
Short Reports/Letters
Adapt expectations for brevity
Ensure core findings are still rigorous and significant
Verify that format is appropriate for findings
Preprints
Recognize that these have not undergone formal peer review
May be less polished than journal submissions
Still apply rigorous standards for scientific validity
Consider providing constructive feedback to help authors improve before journal submission
Presentations and Slide Decks
⚠️ CRITICAL: For presentations, NEVER read the PDF directly. ALWAYS convert to images first.
When reviewing scientific presentations (PowerPoint, Beamer, slide decks):
Mandatory Image-Based Review Workflow
NEVER attempt to read presentation PDFs directly - this causes buffer overflow errors and doesn't show visual formatting issues.
Read and inspect EACH slide image file sequentially
Document issues with specific slide numbers
Provide feedback on visual formatting and content
Print when starting review:
[HH:MM:SS] PEER REVIEW: Presentation detected - converting to images for review
[HH:MM:SS] PDF REVIEW: NEVER reading PDF directly - using image-based inspection
Presentation-Specific Evaluation Criteria
Visual Design and Readability:
Text is large enough (minimum 18pt, ideally 24pt+ for body text)
High contrast between text and background (4.5:1 minimum, 7:1 preferred)
Color scheme is professional and colorblind-accessible
Consistent visual design across all slides
White space is adequate (not cramped)
Fonts are clear and professional
Layout and Formatting (Check EVERY Slide Image):
No text overflow or truncation at slide edges
No element overlaps (text over images, overlapping shapes)
Titles are consistently positioned
Content is properly aligned
Bullets and text are not cut off
Figures fit within slide boundaries
Captions and labels are visible and readable
Content Quality:
One main idea per slide (not overloaded)
Minimal text (3-6 bullets per slide maximum)
Bullet points are concise (5-7 words each)
Figures are simplified and clear (not copy-pasted from papers)
Data visualizations have large, readable labels
Citations are present and properly formatted
Results/data slides dominate the presentation (40-50% of content)
Results presented logically with clear visualizations
Statistical significance indicated appropriately
Conclusions supported by data shown
Limitations acknowledged where appropriate
Future directions or broader impact discussed
Common Presentation Issues to Flag:
Critical Issues (Must Fix):
Text overflow making content unreadable
Font sizes too small (<18pt)
Element overlaps obscuring data
Insufficient contrast (text hard to read)
Figures too complex or illegible
No citations (completely unsupported claims)
Slide count drastically mismatched to duration
Major Issues (Should Fix):
Inconsistent design across slides
Too much text (walls of text, not bullets)
Poorly simplified figures (axis labels too small)
Cramped layout with insufficient white space
Missing key structural elements (no conclusion slide)
Poor color choices (not colorblind-safe)
Minimal results content (<30% of slides)
Minor Issues (Suggestions for Improvement):
Could use more visuals/diagrams
Some slides slightly text-heavy
Minor alignment inconsistencies
Could benefit from more white space
Additional citations would strengthen claims
Color scheme could be more modern
Review Report Format for Presentations
Summary Statement:
Overall impression of presentation quality
Appropriateness for target audience and duration
Key strengths (visual design, content, clarity)
Key weaknesses (formatting issues, content gaps)
Recommendation (ready to present, minor revisions, major revisions)
Layout and Formatting Issues (By Slide Number):
Slide 3: Text overflow - bullet point 4 extends beyond right margin
Slide 7: Element overlap - figure overlaps with caption text
Slide 12: Font size - axis labels too small to read from distance
Slide 18: Alignment - title not centered
Content and Structure Feedback:
Adequacy of background context and citations
Clarity of research question and objectives
Quality of methods summary
Effectiveness of results presentation
Strength of conclusions and implications
Design and Accessibility:
Overall visual appeal and professionalism
Color contrast and readability
Colorblind accessibility
Consistency across slides
Timing and Scope:
Whether slide count matches intended duration
Appropriate level of detail for talk type
Balance between sections
Example Image-Based Review Process
[14:30:00] PEER REVIEW: Starting review of presentation
[14:30:05] PEER REVIEW: Presentation detected - converting to images
[14:30:10] PDF REVIEW: Running pdf_to_images.py on presentation.pdf
[14:30:15] PDF REVIEW: Converted 25 slides to images in review/ directory
[14:30:20] PDF REVIEW: Inspecting slide 1/25 - title slide
[14:30:25] PDF REVIEW: Inspecting slide 2/25 - introduction
...
[14:35:40] PDF REVIEW: Inspecting slide 25/25 - acknowledgments
[14:35:45] PDF REVIEW: Completed image-based review
[14:35:50] PEER REVIEW: Found 8 layout issues, 3 content issues
[14:35:55] PEER REVIEW: Generating structured feedback by slide number
Remember: For presentations, the visual inspection via images is MANDATORY. Never attempt to read presentation PDFs as text - it will fail and miss all visual formatting issues.
Resources
This skill includes reference materials to support comprehensive peer review:
references/reporting_standards.md
Guidelines for major reporting standards across disciplines (CONSORT, PRISMA, ARRIVE, MIAME, STROBE, etc.) to evaluate completeness of methods and results reporting.
references/common_issues.md
Catalog of frequent methodological and statistical issues encountered in peer review, with guidance on identifying and addressing them.
Major concerns are clearly identified and justified
Suggested revisions are specific and actionable
Minor issues are noted but properly categorized
Statistical methods have been evaluated
Reproducibility and data availability assessed
Ethical considerations verified
Figures and tables evaluated for quality and integrity
Writing quality assessed
Tone is constructive and professional throughout
Review is thorough but proportionate to manuscript scope
Recommendation is consistent with identified issues
How do I install peer-review?
Download skills/04-K-Dense-AI-claude-scientific-writer/peer-review/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does peer-review live?
The publisher keeps it at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.
Which agents can use peer-review?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.