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:

Clinical Case Reports - CARE-compliant case reports for medical journals
Diagnostic Reports - Radiology (ACR), pathology (CAP), laboratory reports
Clinical Trial Reports - SAE reports, CSRs, protocol deviations, DSMB reports
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:

Individual Patient Treatment Plans
- Personalized treatment protocols for specific conditions
- Medication dosing, monitoring schedules, follow-up plans
- HIPAA-compliant de-identification
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
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:

Detects relevant skills: Based on your request, Claude identifies which skills to use
Loads resources: Accesses reference materials, scripts, and templates
Applies best practices: Follows the guidelines and standards in each skill
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:

Create a new directory in .claude/skills/
Add a SKILL.md file with your skill definition
Optionally add references/, scripts/, and assets/ subdirectories
Restart the CLI

The new skill will be automatically loaded and available.

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Available Skills

Writing Skills

1. Scientific Writing

2. Literature Review

3. Peer Review

4. Scholar Evaluation

5. Research Grants

6. Clinical Reports

Writing a Clinical Case Report

Generating Diagnostic Reports

Clinical Trial Documentation

Patient Documentation

Validation and Compliance

7. Clinical Decision Support

Individual Treatment Plan

Patient Cohort Analysis

Treatment Recommendation Report

Biomarker Report

Validation

8. LaTeX Research Posters (DEFAULT)

9. Scientific Slides and Presentations

Conference Talk

Seminar Presentation

Thesis Defense

Visual Validation

Timing Check

10. Scientific Schematics and Diagrams

11. Market Research Reports

Generate Market Research Report

Market Sizing Analysis

Competitive Landscape Report

Document Manipulation Skills

12. MarkItDown - Universal File to Markdown Converter

13. DOCX (Word Documents)

14. PDF Documents

15. PPTX (PowerPoint Presentations)

16. XLSX (Excel Spreadsheets)

How Skills Are Used

Skill Integration

Example Usage

Using Scientific Writing Skill

Using Literature Review Skill

Using Document Skills

Using MarkItDown Skill

Using Peer Review Skill

Using Scholar Evaluation Skill

Using Research Grants Skill

Using Scientific Schematics Skill

11. Venue Templates

Query Template for a Journal

Get Conference Paper Template

Grant Proposal Template

Conference Poster

Format Validation

Adding Custom Skills