clinical-decision-support

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. category biology 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: Patient Cohort Analysis - Biomarker-stratified group analyses with statistical outcome comparisons 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: Generate at minimum ONE schematic or diagram (e.g., clinical decision algorithm, treatment pathway, or biomarker stratification tree) For cohort analyses: include patient flow diagram 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: python skills/scientific-schematics/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): Document Title and Type Main title (e.g., "Biomarker-Stratified Cohort Analysis" or "Evidence-Based Treatment Recommendations") Subtitle with disease state and focus 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 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: \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: Report Information Box : Disease state, guideline version/date, target population Key Recommendations Box (green): Top 3-5 GRADE-graded recommendations by line of therapy Biomarker Decision Criteria Box (blue): Key molecular markers influencing treatment selection Evidence Summary Box (gray): Major trials supporting recommendations (e.g., KEYNOTE-189, FLAURA) 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.