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package/bin/skills/clinical-decision-support/SKILL.md

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----
-name: clinical-decision-support
-description: "Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis."
-allowed-tools: [Read, Write, Edit, Bash]
----
-
-# Clinical Decision Support Documents
-
-## Description
-
-Generate professional clinical decision support (CDS) documents for pharmaceutical companies, clinical researchers, and medical decision-makers. This skill specializes in analytical, evidence-based documents that inform treatment strategies and drug development:
-
-1. **Patient Cohort Analysis** - Biomarker-stratified group analyses with statistical outcome comparisons
-2. **Treatment Recommendation Reports** - Evidence-based clinical guidelines with GRADE grading and decision algorithms
-
-All documents are generated as publication-ready LaTeX/PDF files optimized for pharmaceutical research, regulatory submissions, and clinical guideline development.
-
-**Note:** For individual patient treatment plans at the bedside, use the `treatment-plans` skill instead. This skill focuses on group-level analyses and evidence synthesis for pharmaceutical/research settings.
-
-**Writing Style:** For publication-ready documents targeting medical journals, consult the **venue-templates** skill's `medical_journal_styles.md` for guidance on structured abstracts, evidence language, and CONSORT/STROBE compliance.
-
-## Capabilities
-
-### Document Types
-
-**Patient Cohort Analysis**
-- Biomarker-based patient stratification (molecular subtypes, gene expression, IHC)
-- Molecular subtype classification (e.g., GBM mesenchymal-immune-active vs proneural, breast cancer subtypes)
-- Outcome metrics with statistical analysis (OS, PFS, ORR, DOR, DCR)
-- Statistical comparisons between subgroups (hazard ratios, p-values, 95% CI)
-- Survival analysis with Kaplan-Meier curves and log-rank tests
-- Efficacy tables and waterfall plots
-- Comparative effectiveness analyses
-- Pharmaceutical cohort reporting (trial subgroups, real-world evidence)
-
-**Treatment Recommendation Reports**
-- Evidence-based treatment guidelines for specific disease states
-- Strength of recommendation grading (GRADE system: 1A, 1B, 2A, 2B, 2C)
-- Quality of evidence assessment (high, moderate, low, very low)
-- Treatment algorithm flowcharts with TikZ diagrams
-- Line-of-therapy sequencing based on biomarkers
-- Decision pathways with clinical and molecular criteria
-- Pharmaceutical strategy documents
-- Clinical guideline development for medical societies
-
-### Clinical Features
-
-- **Biomarker Integration**: Genomic alterations (mutations, CNV, fusions), gene expression signatures, IHC markers, PD-L1 scoring
-- **Statistical Analysis**: Hazard ratios, p-values, confidence intervals, survival curves, Cox regression, log-rank tests
-- **Evidence Grading**: GRADE system (1A/1B/2A/2B/2C), Oxford CEBM levels, quality of evidence assessment
-- **Clinical Terminology**: SNOMED-CT, LOINC, proper medical nomenclature, trial nomenclature
-- **Regulatory Compliance**: HIPAA de-identification, confidentiality headers, ICH-GCP alignment
-- **Professional Formatting**: Compact 0.5in margins, color-coded recommendations, publication-ready, suitable for regulatory submissions
-
-## Pharmaceutical and Research Use Cases
-
-This skill is specifically designed for pharmaceutical and clinical research applications:
-
-**Drug Development**
-- **Phase 2/3 Trial Analyses**: Biomarker-stratified efficacy and safety analyses
-- **Subgroup Analyses**: Forest plots showing treatment effects across patient subgroups
-- **Companion Diagnostic Development**: Linking biomarkers to drug response
-- **Regulatory Submissions**: IND/NDA documentation with evidence summaries
-
-**Medical Affairs**
-- **KOL Education Materials**: Evidence-based treatment algorithms for thought leaders
-- **Medical Strategy Documents**: Competitive landscape and positioning strategies
-- **Advisory Board Materials**: Cohort analyses and treatment recommendation frameworks
-- **Publication Planning**: Manuscript-ready analyses for peer-reviewed journals
-
-**Clinical Guidelines**
-- **Guideline Development**: Evidence synthesis with GRADE methodology for specialty societies
-- **Consensus Recommendations**: Multi-stakeholder treatment algorithm development
-- **Practice Standards**: Biomarker-based treatment selection criteria
-- **Quality Measures**: Evidence-based performance metrics
-
-**Real-World Evidence**
-- **RWE Cohort Studies**: Retrospective analyses of patient cohorts from EMR data
-- **Comparative Effectiveness**: Head-to-head treatment comparisons in real-world settings
-- **Outcomes Research**: Long-term survival and safety in clinical practice
-- **Health Economics**: Cost-effectiveness analyses by biomarker subgroup
-
-## When to Use
-
-Use this skill when you need to:
-
-- **Analyze patient cohorts** stratified by biomarkers, molecular subtypes, or clinical characteristics
-- **Generate treatment recommendation reports** with evidence grading for clinical guidelines or pharmaceutical strategies
-- **Compare outcomes** between patient subgroups with statistical analysis (survival, response rates, hazard ratios)
-- **Produce pharmaceutical research documents** for drug development, clinical trials, or regulatory submissions
-- **Develop clinical practice guidelines** with GRADE evidence grading and decision algorithms
-- **Document biomarker-guided therapy selection** at the population level (not individual patients)
-- **Synthesize evidence** from multiple trials or real-world data sources
-- **Create clinical decision algorithms** with flowcharts for treatment sequencing
-
-**Do NOT use this skill for:**
-- Individual patient treatment plans (use `treatment-plans` skill)
-- Bedside clinical care documentation (use `treatment-plans` skill)
-- Simple patient-specific treatment protocols (use `treatment-plans` skill)
-
-## Visual Enhancement with Scientific Schematics
-
-**⚠️ MANDATORY: Every clinical decision support document MUST include at least 1-2 AI-generated figures using the scientific-schematics skill.**
-
-This is not optional. Clinical decision documents require clear visual algorithms. Before finalizing any document:
-1. Generate at minimum ONE schematic or diagram (e.g., clinical decision algorithm, treatment pathway, or biomarker stratification tree)
-2. For cohort analyses: include patient flow diagram
-3. For treatment recommendations: include decision flowchart
-
-**How to generate figures:**
-- 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
-
-**How to generate schematics:**
-```bash
-python scripts/generate_schematic.py "your diagram description" -o figures/output.png
-```
-
-The AI will automatically:
-- Create publication-quality images with proper formatting
-- Review and refine through multiple iterations
-- Ensure accessibility (colorblind-friendly, high contrast)
-- Save outputs in the figures/ directory
-
-**When to add schematics:**
-- Clinical decision algorithm flowcharts
-- Treatment pathway diagrams
-- Biomarker stratification trees
-- Patient cohort flow diagrams (CONSORT-style)
-- Survival curve visualizations
-- Molecular mechanism diagrams
-- Any complex concept that benefits from visualization
-
-For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
-
----
-
-## Document Structure
-
-**CRITICAL REQUIREMENT: All clinical decision support documents MUST begin with a complete executive summary on page 1 that spans the entire first page before any table of contents or detailed sections.**
-
-### Page 1 Executive Summary Structure
-
-The first page of every CDS document should contain ONLY the executive summary with the following components:
-
-**Required Elements (all on page 1):**
-1. **Document Title and Type**
-   - Main title (e.g., "Biomarker-Stratified Cohort Analysis" or "Evidence-Based Treatment Recommendations")
-   - Subtitle with disease state and focus
-   
-2. **Report Information Box** (using colored tcolorbox)
-   - Document type and purpose
-   - Date of analysis/report
-   - Disease state and patient population
-   - Author/institution (if applicable)
-   - Analysis framework or methodology
-   
-3. **Key Findings Boxes** (3-5 colored boxes using tcolorbox)
-   - **Primary Results** (blue box): Main efficacy/outcome findings
-   - **Biomarker Insights** (green box): Key molecular subtype findings
-   - **Clinical Implications** (yellow/orange box): Actionable treatment implications
-   - **Statistical Summary** (gray box): Hazard ratios, p-values, key statistics
-   - **Safety Highlights** (red box, if applicable): Critical adverse events or warnings
-
-**Visual Requirements:**
-- Use `\thispagestyle{empty}` to remove page numbers from page 1
-- All content must fit on page 1 (before `\newpage`)
-- Use colored tcolorbox environments with different colors for visual hierarchy
-- Boxes should be scannable and highlight most critical information
-- Use bullet points, not narrative paragraphs
-- End page 1 with `\newpage` before table of contents or detailed sections
-
-**Example First Page LaTeX Structure:**
-```latex
-\maketitle
-\thispagestyle{empty}
-
-% Report Information Box
-\begin{tcolorbox}[colback=blue!5!white, colframe=blue!75!black, title=Report Information]
-\textbf{Document Type:} Patient Cohort Analysis\\
-\textbf{Disease State:} HER2-Positive Metastatic Breast Cancer\\
-\textbf{Analysis Date:} \today\\
-\textbf{Population:} 60 patients, biomarker-stratified by HR status
-\end{tcolorbox}
-
-\vspace{0.3cm}
-
-% Key Finding #1: Primary Results
-\begin{tcolorbox}[colback=blue!5!white, colframe=blue!75!black, title=Primary Efficacy Results]
-\begin{itemize}
-    \item Overall ORR: 72\% (95\% CI: 59-83\%)
-    \item Median PFS: 18.5 months (95\% CI: 14.2-22.8)
-    \item Median OS: 35.2 months (95\% CI: 28.1-NR)
-\end{itemize}
-\end{tcolorbox}
-
-\vspace{0.3cm}
-
-% Key Finding #2: Biomarker Insights
-\begin{tcolorbox}[colback=green!5!white, colframe=green!75!black, title=Biomarker Stratification Findings]
-\begin{itemize}
-    \item HR+/HER2+: ORR 68\%, median PFS 16.2 months
-    \item HR-/HER2+: ORR 78\%, median PFS 22.1 months
-    \item HR status significantly associated with outcomes (p=0.041)
-\end{itemize}
-\end{tcolorbox}
-
-\vspace{0.3cm}
-
-% Key Finding #3: Clinical Implications
-\begin{tcolorbox}[colback=orange!5!white, colframe=orange!75!black, title=Clinical Recommendations]
-\begin{itemize}
-    \item Strong efficacy observed regardless of HR status (Grade 1A)
-    \item HR-/HER2+ patients showed numerically superior outcomes
-    \item Treatment recommended for all HER2+ MBC patients
-\end{itemize}
-\end{tcolorbox}
-
-\newpage
-\tableofcontents  % TOC on page 2
-\newpage  % Detailed content starts page 3
-```
-
-### Patient Cohort Analysis (Detailed Sections - Page 3+)
-- **Cohort Characteristics**: Demographics, baseline features, patient selection criteria
-- **Biomarker Stratification**: Molecular subtypes, genomic alterations, IHC profiles
-- **Treatment Exposure**: Therapies received, dosing, treatment duration by subgroup
-- **Outcome Analysis**: Response rates (ORR, DCR), survival data (OS, PFS), DOR
-- **Statistical Methods**: Kaplan-Meier survival curves, hazard ratios, log-rank tests, Cox regression
-- **Subgroup Comparisons**: Biomarker-stratified efficacy, forest plots, statistical significance
-- **Safety Profile**: Adverse events by subgroup, dose modifications, discontinuations
-- **Clinical Recommendations**: Treatment implications based on biomarker profiles
-- **Figures**: Waterfall plots, swimmer plots, survival curves, forest plots
-- **Tables**: Demographics table, biomarker frequency, outcomes by subgroup
-
-### Treatment Recommendation Reports (Detailed Sections - Page 3+)
-
-**Page 1 Executive Summary for Treatment Recommendations should include:**
-1. **Report Information Box**: Disease state, guideline version/date, target population
-2. **Key Recommendations Box** (green): Top 3-5 GRADE-graded recommendations by line of therapy
-3. **Biomarker Decision Criteria Box** (blue): Key molecular markers influencing treatment selection
-4. **Evidence Summary Box** (gray): Major trials supporting recommendations (e.g., KEYNOTE-189, FLAURA)
-5. **Critical Monitoring Box** (orange/red): Essential safety monitoring requirements
-
-**Detailed Sections (Page 3+):**
-- **Clinical Context**: Disease state, epidemiology, current treatment landscape
-- **Target Population**: Patient characteristics, biomarker criteria, staging
-- **Evidence Review**: Systematic literature synthesis, guideline summary, trial data
-- **Treatment Options**: Available therapies with mechanism of action
-- **Evidence Grading**: GRADE assessment for each recommendation (1A, 1B, 2A, 2B, 2C)
-- **Recommendations by Line**: First-line, second-line, subsequent therapies
-- **Biomarker-Guided Selection**: Decision criteria based on molecular profiles
-- **Treatment Algorithms**: TikZ flowcharts showing decision pathways
-- **Monitoring Protocol**: Safety assessments, efficacy monitoring, dose modifications
-- **Special Populations**: Elderly, renal/hepatic impairment, comorbidities
-- **References**: Full bibliography with trial names and citations
-
-## Output Format
-
-**MANDATORY FIRST PAGE REQUIREMENT:**
-- **Page 1**: Full-page executive summary with 3-5 colored tcolorbox elements
-- **Page 2**: Table of contents (optional)
-- **Page 3+**: Detailed sections with methods, results, figures, tables
-
-**Document Specifications:**
-- **Primary**: LaTeX/PDF with 0.5in margins for compact, data-dense presentation
-- **Length**: Typically 5-15 pages (1 page executive summary + 4-14 pages detailed content)
-- **Style**: Publication-ready, pharmaceutical-grade, suitable for regulatory submissions
-- **First Page**: Always a complete executive summary spanning entire page 1 (see Document Structure section)
-
-**Visual Elements:**
-- **Colors**: 
-  - Page 1 boxes: blue=data/information, green=biomarkers/recommendations, yellow/orange=clinical implications, red=warnings
-  - Recommendation boxes (green=strong recommendation, yellow=conditional, blue=research needed)
-  - Biomarker stratification (color-coded molecular subtypes)
-  - Statistical significance (color-coded p-values, hazard ratios)
-- **Tables**: 
-  - Demographics with baseline characteristics
-  - Biomarker frequency by subgroup
-  - Outcomes table (ORR, PFS, OS, DOR by molecular subtype)
-  - Adverse events by cohort
-  - Evidence summary tables with GRADE ratings
-- **Figures**: 
-  - Kaplan-Meier survival curves with log-rank p-values and number at risk tables
-  - Waterfall plots showing best response by patient
-  - Forest plots for subgroup analyses with confidence intervals
-  - TikZ decision algorithm flowcharts
-  - Swimmer plots for individual patient timelines
-- **Statistics**: Hazard ratios with 95% CI, p-values, median survival times, landmark survival rates
-- **Compliance**: De-identification per HIPAA Safe Harbor, confidentiality notices for proprietary data
-
-## Integration
-
-This skill integrates with:
-- **scientific-writing**: Citation management, statistical reporting, evidence synthesis
-- **clinical-reports**: Medical terminology, HIPAA compliance, regulatory documentation
-- **scientific-schematics**: TikZ flowcharts for decision algorithms and treatment pathways
-- **treatment-plans**: Individual patient applications of cohort-derived insights (bidirectional)
-
-## Key Differentiators from Treatment-Plans Skill
-
-**Clinical Decision Support (this skill):**
-- **Audience**: Pharmaceutical companies, clinical researchers, guideline committees, medical affairs
-- **Scope**: Population-level analyses, evidence synthesis, guideline development
-- **Focus**: Biomarker stratification, statistical comparisons, evidence grading
-- **Output**: Multi-page analytical documents (5-15 pages typical) with extensive figures and tables
-- **Use Cases**: Drug development, regulatory submissions, clinical practice guidelines, medical strategy
-- **Example**: "Analyze 60 HER2+ breast cancer patients by hormone receptor status with survival outcomes"
-
-**Treatment-Plans Skill:**
-- **Audience**: Clinicians, patients, care teams
-- **Scope**: Individual patient care planning
-- **Focus**: SMART goals, patient-specific interventions, monitoring plans
-- **Output**: Concise 1-4 page actionable care plans
-- **Use Cases**: Bedside clinical care, EMR documentation, patient-centered planning
-- **Example**: "Create treatment plan for a 55-year-old patient with newly diagnosed type 2 diabetes"
-
-**When to use each:**
-- Use **clinical-decision-support** for: cohort analyses, biomarker stratification studies, treatment guideline development, pharmaceutical strategy documents
-- Use **treatment-plans** for: individual patient care plans, treatment protocols for specific patients, bedside clinical documentation
-
-## Example Usage
-
-### Patient Cohort Analysis
-
-**Example 1: NSCLC Biomarker Stratification**
-```
-> Analyze a cohort of 45 NSCLC patients stratified by PD-L1 expression (<1%, 1-49%, ≥50%) 
-> receiving pembrolizumab. Include outcomes: ORR, median PFS, median OS with hazard ratios 
-> comparing PD-L1 ≥50% vs <50%. Generate Kaplan-Meier curves and waterfall plot.
-```
-
-**Example 2: GBM Molecular Subtype Analysis**
-```
-> Generate cohort analysis for 30 GBM patients classified into Cluster 1 (Mesenchymal-Immune-Active) 
-> and Cluster 2 (Proneural) molecular subtypes. Compare outcomes including median OS, 6-month PFS rate, 
-> and response to TMZ+bevacizumab. Include biomarker profile table and statistical comparison.
-```
-
-**Example 3: Breast Cancer HER2 Cohort**
-```
-> Analyze 60 HER2-positive metastatic breast cancer patients treated with trastuzumab-deruxtecan, 
-> stratified by prior trastuzumab exposure (yes/no). Include ORR, DOR, median PFS with forest plot 
-> showing subgroup analyses by hormone receptor status, brain metastases, and number of prior lines.
-```
-
-### Treatment Recommendation Report
-
-**Example 1: HER2+ Metastatic Breast Cancer Guidelines**
-```
-> Create evidence-based treatment recommendations for HER2-positive metastatic breast cancer including 
-> biomarker-guided therapy selection. Use GRADE system to grade recommendations for first-line 
-> (trastuzumab+pertuzumab+taxane), second-line (trastuzumab-deruxtecan), and third-line options. 
-> Include decision algorithm flowchart based on brain metastases, hormone receptor status, and prior therapies.
-```
-
-**Example 2: Advanced NSCLC Treatment Algorithm**
-```
-> Generate treatment recommendation report for advanced NSCLC based on PD-L1 expression, EGFR mutation, 
-> ALK rearrangement, and performance status. Include GRADE-graded recommendations for each molecular subtype, 
-> TikZ flowchart for biomarker-directed therapy selection, and evidence tables from KEYNOTE-189, FLAURA, 
-> and CheckMate-227 trials.
-```
-
-**Example 3: Multiple Myeloma Line-of-Therapy Sequencing**
-```
-> Create treatment algorithm for newly diagnosed multiple myeloma through relapsed/refractory setting. 
-> Include GRADE recommendations for transplant-eligible vs ineligible, high-risk cytogenetics considerations, 
-> and sequencing of daratumumab, carfilzomib, and CAR-T therapy. Provide flowchart showing decision points 
-> at each line of therapy.
-```
-
-## Key Features
-
-### Biomarker Classification
-- Genomic: Mutations, CNV, gene fusions
-- Expression: RNA-seq, IHC scores
-- Molecular subtypes: Disease-specific classifications
-- Clinical actionability: Therapy selection guidance
-
-### Outcome Metrics
-- Survival: OS (overall survival), PFS (progression-free survival)
-- Response: ORR (objective response rate), DOR (duration of response), DCR (disease control rate)
-- Quality: ECOG performance status, symptom burden
-- Safety: Adverse events, dose modifications
-
-### Statistical Methods
-- Survival analysis: Kaplan-Meier curves, log-rank tests
-- Group comparisons: t-tests, chi-square, Fisher's exact
-- Effect sizes: Hazard ratios, odds ratios with 95% CI
-- Significance: p-values, multiple testing corrections
-
-### Evidence Grading
-
-**GRADE System**
-- **1A**: Strong recommendation, high-quality evidence
-- **1B**: Strong recommendation, moderate-quality evidence  
-- **2A**: Weak recommendation, high-quality evidence
-- **2B**: Weak recommendation, moderate-quality evidence
-- **2C**: Weak recommendation, low-quality evidence
-
-**Recommendation Strength**
-- **Strong**: Benefits clearly outweigh risks
-- **Conditional**: Trade-offs exist, patient values important
-- **Research**: Insufficient evidence, clinical trials needed
-
-## Best Practices
-
-### For Cohort Analyses
-
-1. **Patient Selection Transparency**: Clearly document inclusion/exclusion criteria, patient flow, and reasons for exclusions
-2. **Biomarker Clarity**: Specify assay methods, platforms (e.g., FoundationOne, Caris), cut-points, and validation status
-3. **Statistical Rigor**: 
-   - Report hazard ratios with 95% confidence intervals, not just p-values
-   - Include median follow-up time for survival analyses
-   - Specify statistical tests used (log-rank, Cox regression, Fisher's exact)
-   - Account for multiple comparisons when appropriate
-4. **Outcome Definitions**: Use standard criteria:
-   - Response: RECIST 1.1, iRECIST for immunotherapy
-   - Adverse events: CTCAE version 5.0
-   - Performance status: ECOG or Karnofsky
-5. **Survival Data Presentation**:
-   - Median OS/PFS with 95% CI
-   - Landmark survival rates (6-month, 12-month, 24-month)
-   - Number at risk tables below Kaplan-Meier curves
-   - Censoring clearly indicated
-6. **Subgroup Analyses**: Pre-specify subgroups; clearly label exploratory vs pre-planned analyses
-7. **Data Completeness**: Report missing data and how it was handled
-
-### For Treatment Recommendation Reports
-
-1. **Evidence Grading Transparency**: 
-   - Use GRADE system consistently (1A, 1B, 2A, 2B, 2C)
-   - Document rationale for each grade
-   - Clearly state quality of evidence (high, moderate, low, very low)
-2. **Comprehensive Evidence Review**: 
-   - Include phase 3 randomized trials as primary evidence
-   - Supplement with phase 2 data for emerging therapies
-   - Note real-world evidence and meta-analyses
-   - Cite trial names (e.g., KEYNOTE-189, CheckMate-227)
-3. **Biomarker-Guided Recommendations**:
-   - Link specific biomarkers to therapy recommendations
-   - Specify testing methods and validated assays
-   - Include FDA/EMA approval status for companion diagnostics
-4. **Clinical Actionability**: Every recommendation should have clear implementation guidance
-5. **Decision Algorithm Clarity**: TikZ flowcharts should be unambiguous with clear yes/no decision points
-6. **Special Populations**: Address elderly, renal/hepatic impairment, pregnancy, drug interactions
-7. **Monitoring Guidance**: Specify safety labs, imaging, and frequency
-8. **Update Frequency**: Date recommendations and plan for periodic updates
-
-### General Best Practices
-
-1. **First Page Executive Summary (MANDATORY)**: 
-   - ALWAYS create a complete executive summary on page 1 that spans the entire first page
-   - Use 3-5 colored tcolorbox elements to highlight key findings
-   - No table of contents or detailed sections on page 1
-   - Use `\thispagestyle{empty}` and end with `\newpage`
-   - This is the single most important page - it should be scannable in 60 seconds
-2. **De-identification**: Remove all 18 HIPAA identifiers before document generation (Safe Harbor method)
-3. **Regulatory Compliance**: Include confidentiality notices for proprietary pharmaceutical data
-4. **Publication-Ready Formatting**: Use 0.5in margins, professional fonts, color-coded sections
-5. **Reproducibility**: Document all statistical methods to enable replication
-6. **Conflict of Interest**: Disclose pharmaceutical funding or relationships when applicable
-7. **Visual Hierarchy**: Use colored boxes consistently (blue=data, green=biomarkers, yellow/orange=recommendations, red=warnings)
-
-## References
-
-See the `references/` directory for detailed guidance on:
-- Patient cohort analysis and stratification methods
-- Treatment recommendation development
-- Clinical decision algorithms
-- Biomarker classification and interpretation
-- Outcome analysis and statistical methods
-- Evidence synthesis and grading systems
-
-## Templates
-
-See the `assets/` directory for LaTeX templates:
-- `cohort_analysis_template.tex` - Biomarker-stratified patient cohort analysis with statistical comparisons
-- `treatment_recommendation_template.tex` - Evidence-based clinical practice guidelines with GRADE grading
-- `clinical_pathway_template.tex` - TikZ decision algorithm flowcharts for treatment sequencing
-- `biomarker_report_template.tex` - Molecular subtype classification and genomic profile reports
-- `evidence_synthesis_template.tex` - Systematic evidence review and meta-analysis summaries
-
-**Template Features:**
-- 0.5in margins for compact presentation
-- Color-coded recommendation boxes
-- Professional tables for demographics, biomarkers, outcomes
-- Built-in support for Kaplan-Meier curves, waterfall plots, forest plots
-- GRADE evidence grading tables
-- Confidentiality headers for pharmaceutical documents
-
-## Scripts
-
-See the `scripts/` directory for analysis and visualization tools:
-- `generate_survival_analysis.py` - Kaplan-Meier curve generation with log-rank tests, hazard ratios, 95% CI
-- `create_waterfall_plot.py` - Best response visualization for cohort analyses
-- `create_forest_plot.py` - Subgroup analysis visualization with confidence intervals
-- `create_cohort_tables.py` - Demographics, biomarker frequency, and outcomes tables
-- `build_decision_tree.py` - TikZ flowchart generation for treatment algorithms
-- `biomarker_classifier.py` - Patient stratification algorithms by molecular subtype
-- `calculate_statistics.py` - Hazard ratios, Cox regression, log-rank tests, Fisher's exact
-- `validate_cds_document.py` - Quality and compliance checks (HIPAA, statistical reporting standards)
-- `grade_evidence.py` - Automated GRADE assessment helper for treatment recommendations
-