Available Skills

Available Skills

Scientific Writer is a deep research and writing tool that combines AI-driven deep research with well-formatted written outputs. The skills below power this capability—from conducting literature searches and verifying citations to generating publication-ready documents in various formats.

This document provides an overview of all skills available in the Scientific Writer CLI.

Writing Skills

1. Scientific Writing

Location: .claude/skills/scientific-writing/

Capabilities:

• IMRaD structure guidance (Introduction, Methods, Results, and Discussion)
• Citation styles (APA, MLA, Chicago, Nature, Science, etc.)
• Figure and table formatting best practices
• Reporting guidelines for various study types
• Writing principles for clarity, precision, and scientific rigor

References:

• citation_styles.md: Comprehensive guide to major citation formats
• figures_tables.md: Best practices for presenting data
• imrad_structure.md: Detailed guidance on each section
• reporting_guidelines.md: Standards for clinical trials, observational studies, etc.
• writing_principles.md: Core principles of scientific communication

2. Literature Review

Location: .claude/skills/literature-review/

Capabilities:

• Conducting systematic literature searches
• Database search strategies (PubMed, Web of Science, etc.)
• Citation management and verification
• Review synthesis and organization
• PDF generation for literature summaries

References:

• citation_styles.md: Citation formatting guidelines
• database_strategies.md: Effective search strategies

Scripts:

• search_databases.py: Automated database searching
• verify_citations.py: Citation verification tools
• generate_pdf.py: PDF generation for reviews

Assets:

• review_template.md: Template for literature review documents

3. Peer Review

Location: .claude/skills/peer-review/

Capabilities:

• Identifying common issues in scientific manuscripts
• Evaluating reporting standards compliance
• Providing constructive feedback
• Assessing methodology and statistical analysis
• Checking adherence to journal guidelines

References:

• common_issues.md: Frequently found problems in manuscripts
• reporting_standards.md: Required elements for different study types

4. Scholar Evaluation

Location: .claude/skills/scholar-evaluation/

Capabilities:

• Systematic quantitative evaluation across 8 dimensions using ScholarEval framework
• Scoring research papers, proposals, and literature reviews (1-5 scale)
• Assessing publication readiness for target venues
• Providing prioritized, actionable feedback with evidence-based recommendations
• Identifying strengths and weaknesses across problem formulation, literature review, methodology, data collection, analysis, results, writing quality, and citations
• Generating comprehensive evaluation reports with dimension scores

References:

• evaluation_framework.md: Detailed rubrics and quality indicators for all 8 evaluation dimensions

Scripts:

• calculate_scores.py: Calculate aggregate scores from dimension ratings, generate evaluation reports

Features:

• Research-backed framework (ScholarEval methodology from arXiv:2510.16234)
• Quantitative scoring (1-5 scale per dimension) with weighted averaging
• Dimension-specific rubrics for consistent evaluation
• Publication readiness assessment
• Strengths/weaknesses identification
• Prioritized recommendations by impact
• Contextual adjustments for work stage, venue, and discipline

When to Use:

• As a complement to peer review for quantitative assessment
• Evaluating publication readiness before submission
• Tracking improvement across multiple revisions
• Benchmarking research quality against established criteria
• Providing structured feedback for academic work

Key Guidance:

• Complements peer-review skill with systematic quantitative approach
• Evaluates across 8 dimensions: Problem Formulation, Literature Review, Methodology, Data Collection, Analysis, Results, Writing Quality, Citations
• Scores range from 1 (Poor) to 5 (Excellent)
• Overall assessment thresholds: 4.5+ (Exceptional/Top-tier), 4.0-4.4 (Strong/Minor revisions), 3.5-3.9 (Good/Major revisions), 3.0-3.4 (Acceptable/Significant revisions), <3.0 (Needs major rework)

5. Research Grants

Location: .claude/skills/research-grants/

Capabilities:

• Writing competitive research proposals for NSF, NIH, DOE, and DARPA
• Agency-specific formatting and requirements
• Review criteria understanding (Intellectual Merit, Broader Impacts, Significance, Innovation)
• Budget preparation and justification
• Specific Aims pages (NIH)
• Project Summaries (NSF)
• Broader Impacts strategies
• Technology transition planning (DOE, DARPA)
• Resubmission strategies

Focus Agencies:

• NSF: National Science Foundation (Intellectual Merit + Broader Impacts)
• NIH: National Institutes of Health (R01, R21, K awards, etc.)
• DOE: Department of Energy (Office of Science, ARPA-E, EERE)
• DARPA: Defense Advanced Research Projects Agency (BAAs, SBIR)

References:

• nsf_guidelines.md: NSF proposal structure, broader impacts, review criteria
• nih_guidelines.md: NIH mechanisms, specific aims, research strategy
• doe_guidelines.md: DOE programs, TRLs, cost sharing, lab partnerships
• darpa_guidelines.md: DARPA structure, Heilmeier Catechism, PM engagement
• broader_impacts.md: Comprehensive NSF broader impacts strategies
• specific_aims_guide.md: Complete guide to NIH Specific Aims page

Assets/Templates:

• nsf_project_summary_template.md: NSF Project Summary with Overview, Intellectual Merit, Broader Impacts
• nih_specific_aims_template.md: NIH Specific Aims page template
• budget_justification_template.md: Budget justification with agency-specific examples

Features:

• Agency-specific review criteria and scoring systems
• Success rates and funding trends by agency
• Timeline planning and milestone development
• Budget preparation with personnel, equipment, travel, supplies
• Broader impacts with measurable outcomes (NSF)
• Preliminary data integration (NIH)
• National laboratory collaboration (DOE)
• Technology transition and commercialization (DOE, DARPA)
• Resubmission and reviewer response strategies

Key Guidance:

• NSF: Equally weighted Intellectual Merit and Broader Impacts (must be substantive)
• NIH: Specific Aims page is the most critical component (1 page)
• DOE: Energy relevance, TRLs, cost sharing, commercialization pathway
• DARPA: High-risk/high-reward, Heilmeier Catechism, PM engagement essential

6. Clinical Reports

Location: .claude/skills/clinical-reports/

Capabilities:

• Writing clinical case reports following CARE (CAse REport) guidelines for journal publication
• Creating diagnostic reports (radiology, pathology, laboratory) with professional standards
• Documenting clinical trial data (SAE reports, Clinical Study Reports per ICH-E3)
• Patient clinical documentation (SOAP notes, H&P, discharge summaries)
• HIPAA compliance and de-identification verification
• Regulatory compliance (FDA 21 CFR Part 11, ICH-GCP)
• Medical terminology and coding standards (SNOMED-CT, LOINC, ICD-10, CPT)
• Quality assurance and validation

Four Major Report Types:

1. Clinical Case Reports - CARE-compliant case reports for medical journals
2. Diagnostic Reports - Radiology (ACR), pathology (CAP), laboratory reports
3. Clinical Trial Reports - SAE reports, CSRs, protocol deviations, DSMB reports
4. Patient Documentation - SOAP notes, H&P, discharge summaries, consultation notes

References:

• case_report_guidelines.md: CARE guidelines, journal requirements, de-identification
• diagnostic_reports_standards.md: ACR/CAP/CLSI standards, structured reporting
• clinical_trial_reporting.md: ICH-E3, CONSORT, SAE reporting, MedDRA coding
• patient_documentation.md: SOAP, H&P, discharge summary standards
• regulatory_compliance.md: HIPAA, 21 CFR Part 11, ICH-GCP, FDA requirements
• medical_terminology.md: SNOMED-CT, LOINC, ICD-10, CPT, abbreviations
• data_presentation.md: Clinical tables, figures, Kaplan-Meier curves, forest plots
• peer_review_standards.md: Review criteria for clinical manuscripts

Templates (12 comprehensive templates):

• case_report_template.md: CARE-compliant case report structure
• soap_note_template.md: SOAP progress note format
• history_physical_template.md: Complete H&P template
• discharge_summary_template.md: Hospital discharge summary
• consult_note_template.md: Consultation note format
• radiology_report_template.md: Structured radiology report
• pathology_report_template.md: Surgical pathology with synoptic reporting
• lab_report_template.md: Clinical laboratory report
• clinical_trial_sae_template.md: Serious adverse event report
• clinical_trial_csr_template.md: Clinical study report (ICH-E3)
• quality_checklist.md: QA checklist for all report types
• hipaa_compliance_checklist.md: Privacy compliance verification

Scripts (8 validation and automation tools):

• validate_case_report.py: Check CARE guideline compliance
• check_deidentification.py: Scan for 18 HIPAA identifiers
• validate_trial_report.py: Verify ICH-E3 structure
• format_adverse_events.py: Generate AE summary tables
• generate_report_template.py: Interactive template generator
• extract_clinical_data.py: Parse structured clinical data
• compliance_checker.py: Regulatory compliance verification
• terminology_validator.py: Medical terminology and coding validation

Features:

• Comprehensive coverage of all clinical report types
• Regulatory compliance built-in (HIPAA, FDA, ICH-GCP)
• Professional templates based on industry standards
• Automated validation and quality checking
• Privacy protection and de-identification tools
• Integration with scientific-writing and peer-review skills

Key Guidance:

• Always obtain informed consent for case reports
• Remove all 18 HIPAA identifiers before publication
• Follow CARE guidelines for case reports
• Use structured reporting for diagnostic reports (BI-RADS, Lung-RADS, etc.)
• Meet regulatory timelines for SAE reporting (7-day, 15-day)
• Document medical necessity for billing support
• Maintain ALCOA-CCEA principles for clinical trial data

When to Use:

• Publishing clinical case reports in medical journals
• Writing radiology, pathology, or laboratory reports
• Documenting adverse events in clinical trials
• Preparing regulatory submissions (CSR, IND safety reports)
• Creating patient progress notes and summaries
• Ensuring HIPAA compliance in clinical documentation

Example Usage:

Writing a Clinical Case Report

> Create a clinical case report for a patient with unusual presentation of acute appendicitis

Claude will use the clinical-reports skill to create a CARE-compliant case report with proper de-identification.

Generating Diagnostic Reports

> Generate a radiology report template for chest CT scan
> Create a pathology report for breast biopsy specimen

Claude will use structured reporting templates (ACR, CAP) with appropriate medical terminology.

Clinical Trial Documentation

> Write an SAE report for serious adverse event in phase 3 trial
> Create a clinical study report outline following ICH-E3

Claude will ensure regulatory compliance and proper causality assessment.

Patient Documentation

> Create a SOAP note for follow-up visit
> Generate a discharge summary for heart failure patient

Claude will use standard clinical documentation formats with billing support.

Validation and Compliance

> Check this case report for HIPAA identifiers
> Validate clinical trial report against ICH-E3 structure

Claude will use validation scripts to ensure compliance and quality.

7. Clinical Decision Support

Location: .claude/skills/clinical-decision-support/

Capabilities:

• Generate professional clinical decision support (CDS) documents for medical professionals
• Create patient cohort analyses stratified by biomarkers or clinical characteristics
• Develop evidence-based treatment recommendation reports with GRADE methodology
• Build clinical decision algorithms and pathways with TikZ flowcharts
• Produce biomarker-guided therapy selection reports
• Support three document types: individual treatment plans, cohort analyses, and recommendation reports
• LaTeX/PDF output with compact professional formatting (0.5in margins)

Document Types:

1. Individual Patient Treatment Plans

   • Personalized treatment protocols for specific conditions
   • Medication dosing, monitoring schedules, follow-up plans
   • HIPAA-compliant de-identification

2. Patient Cohort Analysis

   • Biomarker-stratified group analyses (e.g., PD-L1 expression levels, molecular subtypes)
   • Outcome comparisons with statistical testing (OS, PFS, ORR, safety)
   • Pharmaceutical-grade reports for clinical research

3. Treatment Recommendation Reports

   • Evidence-based clinical guidelines with GRADE grading
   • Treatment algorithms and decision pathways
   • Biomarker-guided therapy selection

References (6 comprehensive guides):

• patient_cohort_analysis.md: Stratification methods, biomarkers, outcome metrics, statistical comparisons
• treatment_recommendations.md: Evidence grading (GRADE), treatment sequencing, monitoring protocols
• clinical_decision_algorithms.md: Decision trees, risk stratification tools, TikZ flowcharts
• biomarker_classification.md: Genomic biomarkers, molecular subtypes, companion diagnostics, actionability frameworks
• outcome_analysis.md: Survival analysis (Kaplan-Meier, Cox regression), response assessment (RECIST), statistical methods
• evidence_synthesis.md: Guideline integration (NCCN, ASCO, ESMO), systematic reviews, GRADE methodology

Templates (4 LaTeX templates):

• cohort_analysis_template.tex: Patient group analysis with demographics, biomarker profile, outcomes, statistics
• treatment_recommendation_template.tex: Evidence-based guidelines with color-coded recommendation boxes
• clinical_pathway_template.tex: TikZ flowcharts for clinical decision algorithms (landscape format)
• biomarker_report_template.tex: Comprehensive genomic profiling reports with therapy matching

Scripts (5 analysis tools):

• generate_survival_analysis.py: Kaplan-Meier curves, log-rank tests, hazard ratios, LaTeX table generation
• create_cohort_tables.py: Baseline characteristics, efficacy outcomes, safety tables with statistical tests
• build_decision_tree.py: Automated TikZ flowchart generation from JSON/text specifications
• biomarker_classifier.py: Patient stratification algorithms (PD-L1, HER2, molecular subtypes)
• validate_cds_document.py: Quality checks for evidence citations, GRADE format, HIPAA compliance

Assets:

• example_gbm_cohort.md: GBM molecular subtype analysis example (Mesenchymal-Immune-Active vs Other)
• recommendation_strength_guide.md: GRADE framework guide with examples and wording templates
• color_schemes.tex: Standardized color definitions for recommendations, urgency, biomarkers

Features:

• Evidence-Based: GRADE methodology for recommendation strength and evidence quality
• Biomarker Integration: Genomic alterations, expression profiles, molecular subtypes
• Statistical Rigor: Proper hypothesis testing, confidence intervals, survival analysis
• Professional Output: Compact LaTeX/PDF matching pharmaceutical industry standards
• Guideline Concordance: Integration with NCCN, ASCO, ESMO, AHA/ACC guidelines
• Clinical Actionability: Tier-based classification (FDA-approved, investigational, VUS)

When to Use:

• Creating treatment plans for individual patients
• Analyzing patient cohorts stratified by biomarkers
• Generating evidence-based clinical recommendations
• Producing pharmaceutical-grade clinical analysis documents
• Developing clinical pathways and decision algorithms
• Reporting biomarker-guided therapy selection

Example Usage:

Individual Treatment Plan

> Create a treatment plan for a 55-year-old patient with newly diagnosed type 2 diabetes and hypertension

Claude will generate a personalized treatment protocol with monitoring and follow-up.

Patient Cohort Analysis

> Analyze a cohort of 45 NSCLC patients stratified by PD-L1 expression (<1%, 1-49%, ≥50%) including ORR, PFS, and OS outcomes

> Generate cohort analysis for 30 GBM patients classified into mesenchymal-immune-active and proneural molecular subtypes with treatment outcomes

Claude will create comprehensive cohort reports with biomarker profiles, outcome comparisons, statistical analysis, and clinical recommendations.

Treatment Recommendation Report

> Create evidence-based treatment recommendations for HER2-positive metastatic breast cancer including first-line and second-line options

> Generate treatment algorithm for heart failure management based on NYHA class and ejection fraction with GDMT protocols

Claude will develop recommendation reports with GRADE-graded options, decision algorithms, and monitoring protocols.

Biomarker Report

> Create a genomic profiling report for NSCLC patient with EGFR L858R mutation including FDA-approved therapies and clinical trial matching

Claude will generate biomarker reports with tier-based actionability and personalized treatment recommendations.

Validation

> Validate this cohort analysis document for evidence citations and statistical reporting completeness

Claude will use validation scripts to check quality and compliance.

8. LaTeX Research Posters (DEFAULT)

Location: .claude/skills/latex-posters/

⚠️ This is the DEFAULT skill for all poster requests. Use this unless user explicitly requests PPTX/PowerPoint format.

Capabilities:

• Creating professional research posters using LaTeX (beamerposter, tikzposter, baposter)
• AI-powered visual element generation (generate figures BEFORE assembling poster)
• Conference poster design and layout
• Full-page poster templates with proper spacing
• Color schemes and visual design principles
• Typography and readability optimization
• PDF generation and quality control
• Accessibility and inclusive design
• Poster size configuration (A0, A1, 36×48", etc.)
• Overflow prevention and content density guidelines

References:

• latex_poster_packages.md: Detailed comparison of beamerposter, tikzposter, and baposter
• poster_design_principles.md: Typography, color theory, visual hierarchy, and accessibility
• poster_layout_design.md: Grid systems, spatial organization, and visual flow
• poster_content_guide.md: Content strategy, writing style, and section-specific guidance

Scripts:

• review_poster.sh: Automated PDF quality check script

Assets:

• beamerposter_template.tex: Classic academic poster template
• tikzposter_template.tex: Modern, colorful poster template
• baposter_template.tex: Structured multi-column poster template
• poster_quality_checklist.md: Comprehensive pre-printing checklist

Features:

• AI-Powered Visual Generation: Generate all figures using scientific-schematics before creating poster
• Poster-Size Font Requirements: Guidelines for readable text in AI-generated graphics (72pt+ for key numbers)
• Overflow Prevention: Content limits (5-6 sections max, 300-800 words) to prevent cutoff
• Ensures posters span the full page without excessive margins
• PDF review and quality control guidelines with overflow check
• Automated checking scripts for page size, fonts, and images
• Reduced-scale print testing instructions
• Color contrast and accessibility verification
• Common issues troubleshooting guide

For PPTX/PowerPoint posters: Use pptx-posters skill ONLY when user explicitly requests PPTX format. Located at .claude/skills/pptx-posters/.

9. Scientific Slides and Presentations

Location: .claude/skills/scientific-slides/

Capabilities:

• Create stunning PDF slide decks using Nano Banana Pro AI
• Structure presentations for different contexts (5-60 minute talks)
• AI-generated slides with publication-quality visuals
• Optimize data visualizations for presentation context
• Timing and pacing guidance with practice strategies
• Visual review workflow with automated validation
• Integration with research-lookup for proper citations

Talk Types Supported:

• Conference talks (10-20 min): Brief, focused on key findings
• Academic seminars (45-60 min): Comprehensive, detailed methods
• Thesis defenses (45-60 min): Complete dissertation overview
• Grant pitches (15-20 min): Emphasis on significance and feasibility
• Journal clubs (20-45 min): Critical analysis of published work
• Lightning talks (5 min): Ultra-focused single message

References:

• presentation_structure.md: Structure for all talk types, timing allocation, narrative arc
• slide_design_principles.md: Typography, color theory, layout, accessibility
• data_visualization_slides.md: Simplifying figures for presentations
• talk_types_guide.md: Specific guidance for each presentation type
• visual_review_workflow.md: PDF to images, systematic inspection, iteration

Assets:

• timing_guidelines.md: Comprehensive timing, pacing, and practice strategies

Scripts:

• validate_presentation.py: Check slide count, timing, fonts, file size
• pdf_to_images.py: Convert PDF to images for visual inspection

Features:

• Nano Banana Pro AI: Generate stunning PDF slides with AI-powered visuals
• Research-lookup integration: Automatically gather citations for background and discussion
• Visual validation workflow: Convert to images, inspect systematically, iterate
• Timing guidance: One-slide-per-minute rule with adjustments
• Design principles: Minimal text (24pt+), high contrast, color-blind safe
• Practice strategies: Systematic rehearsal with timing checkpoints

When to Use:

• Creating any scientific presentation or slide deck
• Preparing conference talks or research seminars
• Developing thesis defense presentations
• Making grant pitch slides
• Building lecture or tutorial presentations
• Converting papers to presentation format

Example Usage:

Conference Talk

> Create a 15-minute conference presentation on my machine learning research

Claude will use research-lookup to gather citations, structure the talk, and generate stunning PDF slides using Nano Banana Pro AI.

Seminar Presentation

> Help me build a 45-minute seminar on CRISPR gene editing with comprehensive methods

Claude will structure a detailed academic seminar with proper citations and timing guidance.

Thesis Defense

> Create slides for my dissertation defense covering three studies

Claude will structure a comprehensive defense presentation following academic standards.

Visual Validation

> Convert my presentation to images and review for layout issues

Claude will use scripts to convert PDF to images and systematically inspect for text overflow, overlap, and design issues.

Timing Check

> Validate my 20-slide presentation for a 15-minute talk

Claude will check if slide count is appropriate and provide timing recommendations.

Key Principles:

• Structure: Spend 40-50% of time on results, follow clear story arc
• Design: Minimal text, large fonts (24pt+), one idea per slide
• Citations: Use research-lookup to gather 8-12 papers for proper context
• Timing: Practice 3-5 times, set checkpoints, never skip conclusions
• Validation: Visual review workflow to catch overflow and overlap issues

10. Scientific Schematics and Diagrams

Location: .claude/skills/scientific-schematics/

Capabilities:

• Create methodology flowcharts (CONSORT diagrams for clinical trials)
• Generate circuit diagrams and electrical schematics
• Visualize biological pathways and signaling cascades
• Design system architecture and block diagrams
• Create process flow diagrams and decision trees
• Network diagrams and graph visualizations
• Publication-quality vector graphics with TikZ/LaTeX
• Programmatic diagram generation with Python (Schemdraw, NetworkX, Matplotlib)

References:

• tikz_guide.md: Comprehensive TikZ syntax, positioning, styles, and techniques
• diagram_types.md: Catalog of scientific diagram types with use cases and examples
• best_practices.md: Publication standards, accessibility, and colorblind-safe design
• python_libraries.md: Guide to Schemdraw, NetworkX, and Matplotlib for programmatic generation

Scripts:

• generate_flowchart.py: Convert text descriptions to TikZ flowcharts
• circuit_generator.py: Generate circuit diagrams using Schemdraw
• pathway_diagram.py: Create biological pathway diagrams with Matplotlib
• compile_tikz.py: Standalone TikZ compilation utility (PDF/PNG output)

Assets:

• tikz_styles.tex: Reusable style definitions with Okabe-Ito colorblind-safe palette
• flowchart_template.tex: CONSORT-style methodology flowchart template
• circuit_template.tex: Electrical circuit diagram template with CircuitikZ
• pathway_template.tex: Biological pathway diagram template
• block_diagram_template.tex: System architecture diagram template

Features:

• Colorblind-safe Okabe-Ito color palette throughout
• Vector graphics for infinite scalability
• LaTeX integration for consistent typography
• Automated flowchart generation from numbered lists
• Publication-ready output (PDF, SVG, PNG)
• Accessible design following WCAG standards
• Grayscale compatibility verification

Use Cases:

• CONSORT diagrams: Participant flow for clinical trials
• Electronics papers: Circuit schematics and signal processing diagrams
• Biology papers: Signaling cascades, metabolic pathways, gene networks
• Engineering papers: System architecture, data flow, block diagrams
• Methodology sections: Study design, data processing pipelines
• Conceptual frameworks: Process flows, decision trees

11. Market Research Reports

Location: .claude/skills/market-research-reports/

Capabilities:

• Generate comprehensive market research reports (50+ pages) in consulting-firm style
• Professional LaTeX formatting with custom market_research.sty style package
• Extensive visual generation (25-30 diagrams per report) using scientific-schematics
• Multi-framework strategic analysis (Porter's Five Forces, PESTLE, SWOT, BCG Matrix)
• TAM/SAM/SOM market sizing with data-driven projections
• Competitive landscape analysis with positioning matrices
• Risk assessment with heatmaps and mitigation frameworks
• Strategic recommendations with implementation roadmaps
• Investment thesis development with financial projections

References:

• report_structure_guide.md: Detailed section-by-section content requirements for all 11 chapters
• visual_generation_guide.md: Complete prompts for generating all 28 standard report visuals
• data_analysis_patterns.md: Templates for Porter's, PESTLE, SWOT, BCG Matrix, TAM/SAM/SOM

Scripts:

• generate_market_visuals.py: Batch generate all standard market report visuals with a single command

Assets:

• market_research.sty: LaTeX style package with professional colors, box environments, and formatting
• market_report_template.tex: Complete 50+ page LaTeX template with all chapters pre-structured
• FORMATTING_GUIDE.md: Quick reference for box environments, colors, tables, and styling

Features:

• Comprehensive Length: Reports designed for 50+ pages with no token constraints
• Visual Density: 25-30 generated images/diagrams (approximately 1 per 2 pages)
• Data-Driven: Deep integration with research-lookup for market data and statistics
• Multi-Framework: Porter's Five Forces, PESTLE, SWOT, BCG Matrix, Value Chain Analysis
• Professional Formatting: Consulting-firm quality typography, colors, and layout
• Actionable Recommendations: Strategic focus with prioritization matrices and implementation roadmaps

Report Structure (50+ Pages):

• Front Matter: Cover page, TOC, Executive Summary (5 pages)
• Core Analysis: Market Overview, Market Size & Growth, Industry Drivers, Competitive Landscape, Customer Analysis, Technology Landscape, Regulatory Environment, Risk Analysis (35 pages)
• Strategic Recommendations: Opportunities, Implementation Roadmap, Investment Thesis (10 pages)
• Back Matter: Methodology, Data Tables, Company Profiles, References (5 pages)

When to Use:

• Creating comprehensive market analysis for investment decisions
• Developing industry reports for strategic planning
• Analyzing competitive landscapes and market dynamics
• Conducting market sizing exercises (TAM/SAM/SOM)
• Evaluating market entry opportunities
• Preparing due diligence materials for M&A activities
• Creating thought leadership content
• Developing go-to-market strategy documentation

Example Usage:

Generate Market Research Report

> Create a comprehensive market research report on the Electric Vehicle Charging Infrastructure market

Claude will use the market-research-reports skill to create a 50+ page professional report with extensive visuals.

Market Sizing Analysis

> Analyze the AI in Healthcare market with TAM/SAM/SOM breakdown and 10-year projections

Claude will provide comprehensive market sizing with growth trajectory charts and regional breakdowns.

Competitive Landscape Report

> Create a competitive landscape analysis for the Cloud Computing market including Porter's Five Forces and positioning matrix

Claude will generate competitive analysis with strategic frameworks and visualizations.

Document Manipulation Skills

12. MarkItDown - Universal File to Markdown Converter

Location: .claude/skills/markitdown/

Capabilities:

• Convert 15+ file formats to Markdown (PDF, DOCX, PPTX, XLSX, images, audio, etc.)
• AI-enhanced image descriptions using advanced vision models
• OCR for scanned documents and images
• Speech-to-text transcription for audio files
• YouTube video transcription extraction
• Batch processing with parallel execution
• Azure Document Intelligence integration for complex PDFs
• Plugin system for custom converters

References:

• api_reference.md: Complete API documentation and class references
• file_formats.md: Format-specific conversion guides and best practices

Scripts:

• batch_convert.py: Parallel batch conversion of multiple files
• convert_with_ai.py: AI-enhanced conversions with custom prompts
• convert_literature.py: Scientific literature conversion with metadata extraction

Assets:

• example_usage.md: Comprehensive examples for common use cases

Features:

• Token-efficient Markdown output optimized for LLM processing
• Supports optional dependencies for specific file formats
• Custom prompts for scientific, medical, and data visualization contexts
• Metadata extraction and organization
• Error handling and robust batch processing
• Integration with scientific workflows

Source: https://github.com/microsoft/markitdown (MIT License)

13. DOCX (Word Documents)

Location: .claude/skills/document-skills/docx/

Capabilities:

• Create and edit Word documents programmatically
• Work with OOXML format
• Manage comments and track changes
• Validate document structure
• Handle templates

Scripts:

• document.py: Core document manipulation
• utilities.py: Helper functions
• OOXML validation and manipulation tools

References:

• docx-js.md: JavaScript integration guide
• ooxml.md: OOXML format specification

14. PDF Documents

Location: .claude/skills/document-skills/pdf/

Capabilities:

• Extract text and metadata from PDFs
• Check bounding boxes and layout
• Work with fillable PDF forms
• Convert PDFs to images
• Extract form field information

Scripts:

• check_bounding_boxes.py: Analyze PDF layout
• check_fillable_fields.py: Identify form fields
• fill_fillable_fields.py: Populate PDF forms
• convert_pdf_to_images.py: PDF to image conversion
• extract_form_field_info.py: Extract form metadata

References:

• forms.md: Working with PDF forms
• reference.md: PDF manipulation reference

15. PPTX (PowerPoint Presentations)

Location: .claude/skills/document-skills/pptx/

Capabilities:

• Create and modify PowerPoint presentations
• Convert HTML to PowerPoint
• Manage slides and layouts
• Work with OOXML format
• Generate thumbnails

Scripts:

• html2pptx.js: HTML to PowerPoint conversion
• inventory.py: Presentation inventory management
• rearrange.py: Slide reordering
• replace.py: Content replacement
• thumbnail.py: Thumbnail generation

References:

• html2pptx.md: HTML conversion guide
• ooxml.md: OOXML format specification

16. XLSX (Excel Spreadsheets)

Location: .claude/skills/document-skills/xlsx/

Capabilities:

• Read and write Excel files
• Manage formulas and calculations
• Handle complex spreadsheet operations
• Recalculate formulas

Scripts:

• recalc.py: Formula recalculation utility

How Skills Are Used

When you interact with the Scientific Writer CLI, Claude automatically:

1. Detects relevant skills: Based on your request, Claude identifies which skills to use
2. Loads resources: Accesses reference materials, scripts, and templates
3. Applies best practices: Follows the guidelines and standards in each skill
4. Executes tools: Uses scripts when needed for document manipulation or data processing

Skill Integration

All skills are loaded from the .claude/skills/ directory and are automatically available when you run the CLI. You don't need to manually select or activate them - Claude will use the appropriate skills based on your requests.

Example Usage

Using Scientific Writing Skill

> Help me structure a methods section for a randomized controlled trial

Claude will use the scientific-writing skill to provide IMRaD-compliant guidance.

Using Literature Review Skill

> Create a literature review on CRISPR gene editing in agriculture

Claude will use literature-review skill to structure a comprehensive review.

Using Document Skills

> Extract the data from Table 1 in results.pdf and create a summary

Claude will use the PDF skill to extract data and potentially the XLSX skill to organize it.

Using MarkItDown Skill

> Convert all PDFs in the literature folder to Markdown

Claude will use the markitdown skill to batch convert files.

> Convert this PowerPoint presentation to Markdown with AI-generated descriptions

Claude will use markitdown with AI enhancement for detailed image descriptions.

Using Peer Review Skill

> Review my discussion section for logical flow and adherence to reporting standards

Claude will use the peer-review skill to provide constructive feedback.

Using Scholar Evaluation Skill

> Evaluate this paper using the ScholarEval framework

Claude will use the scholar-evaluation skill to provide systematic quantitative evaluation across 8 dimensions.

> Assess publication readiness for Nature Machine Intelligence

Claude will evaluate the paper and provide scores and recommendations for submission readiness.

Using Research Grants Skill

> Help me write an NSF proposal for my computational neuroscience research

Claude will use the research-grants skill to provide NSF-specific guidance.

> I need to draft NIH Specific Aims for my cancer immunotherapy R01

Claude will help structure your 1-page specific aims using NIH best practices.

> What should I include in broader impacts for an NSF Materials Research proposal?

Claude will provide substantive broader impacts strategies aligned with NSF criteria.

Using Scientific Schematics Skill

> Create a CONSORT flowchart for my clinical trial showing participant flow from screening (n=500) through randomization to final analysis

Claude will generate a methodology flowchart following CONSORT guidelines.

> Generate a circuit diagram for an RC low-pass filter

Claude will create an electrical circuit schematic using CircuitikZ or Schemdraw.

> Create a biological pathway diagram showing the MAPK signaling cascade from receptor to gene expression

Claude will visualize the signaling pathway with properly styled proteins and activation arrows.

> Design a block diagram showing the architecture of my data acquisition system with sensor, ADC, microcontroller, and wireless transmission

Claude will create a system architecture diagram with labeled components and data flow.

11. Venue Templates

Location: .claude/skills/venue-templates/

Capabilities:

• Query LaTeX templates for 50+ major journals and conferences
• Access grant proposal templates (NSF, NIH, DOE, DARPA)
• Retrieve poster templates for academic conferences
• View formatting requirements and submission guidelines
• Customize templates with author and project information
• Validate document formatting against venue requirements

References:

• journals_formatting.md: Requirements for Nature, Science, PLOS, IEEE, ACM, Cell Press, and other major journals
• conferences_formatting.md: ML, CS, biology conference paper formats (NeurIPS, ICML, ICLR, CVPR, CHI, ISMB, etc.)
• posters_guidelines.md: Poster design, sizes, layout principles, and best practices
• grants_requirements.md: Federal and private grant proposal formats (NSF, NIH, DOE, DARPA)

Scripts:

• query_template.py: Search and retrieve templates by venue name or keywords
• customize_template.py: Customize templates with author information
• validate_format.py: Check document compliance with venue requirements

Assets:

• journals/: LaTeX templates for Nature, Science, PLOS ONE, NeurIPS, and other major venues
• posters/: Academic poster templates (beamerposter, tikzposter, baposter)
• grants/: Grant proposal templates (NSF, NIH Specific Aims, DOE, DARPA)

Features:

• Comprehensive formatting guidelines for major publication venues
• Ready-to-use LaTeX templates with proper structure
• Helper scripts for template discovery and customization
• Formatting validation tools
• Integration with scientific writing workflow

Use Cases:

• Journal submission: Get proper formatting for Nature, Science, PLOS, IEEE, ACM journals
• Conference papers: Templates for NeurIPS, ICML, CVPR, CHI, and other major conferences
• Research posters: Professional poster templates for A0, A1, and US sizes
• Grant proposals: NSF, NIH R01, DOE, DARPA proposal templates with requirements
• Format validation: Check if your document meets venue specifications

Example Usage:

Query Template for a Journal

> I need to submit to Nature

Claude will provide the Nature article template and formatting requirements.

Get Conference Paper Template

> Show me the NeurIPS paper template

Claude will provide the NeurIPS conference paper template with anonymization guidelines.

Grant Proposal Template

> I need an NSF proposal template

Claude will provide the NSF proposal template with all required sections and formatting.

Conference Poster

> Create a research poster for ISMB conference

Claude will provide poster template and size specifications for the conference.

Format Validation

> Check if my paper meets Nature's requirements

Claude can guide you through using the validation script to check formatting compliance.

Adding Custom Skills

To add your own skills:

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