@saibolla/ada 0.1.2

package/skills/clinical-decision-support/assets/treatment_recommendation_template.tex

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+\documentclass[10pt,letterpaper]{article}
+
+% Packages
+\usepackage[margin=0.5in]{geometry}
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{helvet}
+\renewcommand{\familydefault}{\sfdefault}
+\usepackage{xcolor}
+\usepackage{tcolorbox}
+\usepackage{array}
+\usepackage{tabularx}
+\usepackage{booktabs}
+\usepackage{enumitem}
+\usepackage{titlesec}
+\usepackage{fancyhdr}
+\usepackage{multicol}
+\usepackage{graphicx}
+\usepackage{tikz}
+\usetikzlibrary{shapes,arrows,positioning}
+
+% Color definitions
+\definecolor{headerblue}{RGB}{0,102,204}
+\definecolor{stronggreen}{RGB}{0,153,76}
+\definecolor{conditionalyellow}{RGB}{255,193,7}
+\definecolor{researchblue}{RGB}{33,150,243}
+\definecolor{warningred}{RGB}{204,0,0}
+\definecolor{highlightgray}{RGB}{240,240,240}
+
+% Section formatting - compact
+\titleformat{\section}{\normalfont\fontsize{11}{12}\bfseries\color{headerblue}}{\thesection}{0.5em}{}
+\titlespacing*{\section}{0pt}{4pt}{2pt}
+
+\titleformat{\subsection}{\normalfont\fontsize{10}{11}\bfseries}{\thesubsection}{0.5em}{}
+\titlespacing*{\subsection}{0pt}{3pt}{1pt}
+
+% List formatting - ultra compact
+\setlist[itemize]{leftmargin=*,itemsep=0pt,parsep=0pt,topsep=1pt}
+\setlist[enumerate]{leftmargin=*,itemsep=0pt,parsep=0pt,topsep=1pt}
+
+% Remove paragraph indentation
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{2pt}
+
+% Header/footer
+\pagestyle{fancy}
+\fancyhf{}
+\fancyhead[L]{\footnotesize \textbf{Treatment Recommendations: [CONDITION]}}
+\fancyhead[R]{\footnotesize Page \thepage}
+\renewcommand{\headrulewidth}{0.5pt}
+\fancyfoot[C]{\footnotesize Evidence-Based Clinical Guideline - For Professional Use Only}
+
+\begin{document}
+
+% Title block
+\begin{center}
+{\fontsize{14}{16}\selectfont\bfseries\color{headerblue} EVIDENCE-BASED TREATMENT RECOMMENDATIONS}\\[2pt]
+{\fontsize{12}{14}\selectfont\bfseries [Disease/Condition - e.g., HER2+ Metastatic Breast Cancer]}\\[2pt]
+{\fontsize{10}{12}\selectfont [Institution/Organization]}\\[1pt]
+{\fontsize{9}{11}\selectfont Version X.X | Effective Date: [Date] | Next Review: [Date]}
+\end{center}
+
+\vspace{4pt}
+
+% Recommendation Strength Legend
+\begin{tcolorbox}[colback=highlightgray,colframe=black,title=\textbf{Recommendation Strength Key},fonttitle=\bfseries\small,coltitle=black]
+{\small
+\begin{itemize}
+\item \colorbox{stronggreen!30}{\textbf{STRONG (Grade 1)}} - Benefits clearly outweigh risks; most patients should receive intervention
+\item \colorbox{conditionalyellow!30}{\textbf{CONDITIONAL (Grade 2)}} - Trade-offs exist; shared decision-making essential
+\item \colorbox{researchblue!30}{\textbf{RESEARCH (Grade R)}} - Insufficient evidence; clinical trial enrollment preferred
+\end{itemize}
+
+\textbf{Evidence Quality}: \textbf{A} = High (RCTs), \textbf{B} = Moderate (RCTs with limitations), \textbf{C} = Low (observational), \textbf{D} = Very low (expert opinion)
+}
+\end{tcolorbox}
+
+\vspace{2pt}
+
+\section{Clinical Context}
+
+\subsection{Disease Overview}
+
+[Brief description of disease state, epidemiology, natural history]
+
+\subsection{Patient Population}
+
+\textbf{Target Population}:
+\begin{itemize}
+\item [Demographic characteristics - e.g., Adults $\geq$18 years]
+\item [Disease stage/severity - e.g., Metastatic disease, Stage IV]
+\item [Biomarker status - e.g., HER2-positive (IHC 3+ or FISH+)]
+\item [Performance status - e.g., ECOG 0-2]
+\item [Line of therapy - e.g., First-line, previously untreated]
+\end{itemize}
+
+\textbf{Exclusions}:
+\begin{itemize}
+\item [Contraindications to recommended therapies]
+\item [Comorbidities affecting eligibility]
+\end{itemize}
+
+\section{Evidence Review}
+
+\subsection{Key Clinical Trials}
+
+\textbf{[Trial Name 1]} (Author, Journal Year):
+\begin{itemize}
+\item \textbf{Design}: Phase 3 RCT, n=XXX, [Treatment A] vs [Treatment B]
+\item \textbf{Population}: [Key eligibility criteria]
+\item \textbf{Primary Endpoint}: [Outcome] - XX vs XX months (HR X.XX, 95\% CI X.XX-X.XX, p<X.XXX)
+\item \textbf{Secondary Endpoints}: [Additional outcomes]
+\item \textbf{Safety}: Grade 3-4 AEs XX\% vs XX\%
+\item \textbf{Quality}: \textbf{High} (low risk of bias, adequate power, intention-to-treat analysis)
+\end{itemize}
+
+\textbf{[Trial Name 2]} (Author, Journal Year):
+\begin{itemize}
+\item \textbf{Design}: Phase 3 RCT, n=XXX, [Treatment C] vs [Standard of care]
+\item \textbf{Primary Endpoint}: [Outcome and results]
+\item \textbf{Quality}: \textbf{Moderate} (some limitations)
+\end{itemize}
+
+\subsection{Guideline Concordance}
+
+\begin{table}[H]
+\centering
+\small
+\begin{tabular}{lll}
+\toprule
+\textbf{Guideline} & \textbf{Recommendation} & \textbf{Evidence Level} \\
+\midrule
+NCCN vX.XXXX & [Specific recommendation] & Category 1 (preferred) \\
+ASCO Year & [Recommendation] & Strong, Evidence A \\
+ESMO Year & [Recommendation] & Grade I, A \\
+\bottomrule
+\end{tabular}
+\caption{Major guideline recommendations}
+\end{table}
+
+\section{Treatment Options}
+
+\subsection{First-Line Therapy}
+
+\begin{tcolorbox}[enhanced,colback=stronggreen!10,colframe=stronggreen,
+title={\textbf{Option 1: [Regimen Name]} \hfill \colorbox{white}{\textbf{STRONG (1A)}}},
+fonttitle=\bfseries\small,coltitle=black]
+{\small
+\textbf{Regimen}:
+\begin{itemize}
+\item [Drug A]: XX mg [IV/PO] [schedule]
+\item [Drug B]: XX mg [IV/PO] [schedule]
+\item Cycle length: XX days
+\item Duration: Until progression or unacceptable toxicity
+\end{itemize}
+
+\textbf{Evidence Basis}:
+\begin{itemize}
+\item Primary study: [Trial name], n=XXX
+\item Primary outcome: [Endpoint] XX vs XX months (HR X.XX, p<X.XXX)
+\item ORR: XX\% vs XX\% (control)
+\end{itemize}
+
+\textbf{Indications}:
+\begin{itemize}
+\item [Biomarker-defined population or all patients]
+\item [Performance status requirement]
+\item [Organ function requirements]
+\end{itemize}
+
+\textbf{Key Toxicities}:
+\begin{itemize}
+\item Grade 3-4 AEs: XX\%
+\item Common: [List 3-5 most common AEs with incidence]
+\item Serious: [SAEs, discontinuation rate]
+\item Management: [Key mitigation strategies]
+\end{itemize}
+
+\textbf{Monitoring}:
+\begin{itemize}
+\item Labs: [Specific tests, frequency]
+\item Imaging: Every [X weeks] (RECIST v1.1)
+\item Clinical assessment: Every cycle
+\end{itemize}
+
+\textbf{Recommendation Strength}: \textbf{STRONG} - Benefits clearly outweigh risks\\
+\textbf{Evidence Quality}: \textbf{HIGH} - Well-designed RCT with consistent results
+}
+\end{tcolorbox}
+
+\vspace{3pt}
+
+\begin{tcolorbox}[enhanced,colback=conditionalyellow!10,colframe=conditionalyellow,
+title={\textbf{Option 2: [Alternative Regimen]} \hfill \colorbox{white}{\textbf{CONDITIONAL (2B)}}},
+fonttitle=\bfseries\small,coltitle=black]
+{\small
+\textbf{Regimen}: [Dosing details]
+
+\textbf{Evidence Basis}: [Moderate-quality evidence or specific population subset]
+
+\textbf{Indications}: [When to consider this option - e.g., patient preference for oral therapy, specific contraindication to Option 1]
+
+\textbf{Trade-offs}: 
+\begin{itemize}
+\item Advantages: [e.g., Oral administration, better tolerability]
+\item Disadvantages: [e.g., Lower response rate, less survival benefit]
+\end{itemize}
+
+\textbf{Recommendation Strength}: \textbf{CONDITIONAL} - Patient values important in decision\\
+\textbf{Evidence Quality}: \textbf{MODERATE} - Some limitations in evidence base
+}
+\end{tcolorbox}
+
+\vspace{3pt}
+
+\begin{tcolorbox}[enhanced,colback=researchblue!10,colframe=researchblue,
+title={\textbf{Option 3: Clinical Trial} \hfill \colorbox{white}{\textbf{RESEARCH (R)}}},
+fonttitle=\bfseries\small,coltitle=black]
+{\small
+\textbf{Recommendation}: Consider clinical trial enrollment for [specific scenario - e.g., biomarker-selected patients, refractory disease]
+
+\textbf{Available Trials}: [List relevant trials if known, or state "ClinicalTrials.gov search"]
+
+\textbf{Rationale}: [Why clinical trial appropriate - e.g., novel mechanism, unmet medical need, investigational biomarker]
+}
+\end{tcolorbox}
+
+\subsection{Second-Line and Beyond}
+
+\textbf{At Progression on First-Line Therapy}:
+
+\begin{itemize}
+\item \textbf{Biomarker Re-Testing}: [If applicable - e.g., liquid biopsy for resistance mutations]
+\item \textbf{Second-Line Options}:
+  \begin{itemize}
+  \item Preferred: [Regimen] (Evidence level)
+  \item Alternative: [Regimen] (Evidence level)
+  \end{itemize}
+\item \textbf{Third-Line Options}: [Subsequent therapy options]
+\end{itemize}
+
+\section{Special Populations}
+
+\subsection{Elderly Patients ($\geq$70 years)}
+
+\textbf{Considerations}:
+\begin{itemize}
+\item Geriatric assessment recommended (G8 screening tool)
+\item Dose reductions: [Specific adjustments for frail patients]
+\item Monitoring: More frequent assessments for toxicity
+\end{itemize}
+
+\textbf{Regimen Modifications}:
+\begin{itemize}
+\item [Reduced-intensity regimens if appropriate]
+\item [Single-agent vs combination considerations]
+\end{itemize}
+
+\subsection{Renal Impairment}
+
+\begin{table}[H]
+\centering
+\footnotesize
+\begin{tabular}{lll}
+\toprule
+\textbf{eGFR (mL/min/1.73m²)} & \textbf{Category} & \textbf{Dose Adjustment} \\
+\midrule
+$\geq$60 & Normal/Mild & Standard dosing \\
+30-59 & Moderate & [Specific adjustment - e.g., Reduce 25\%] \\
+15-29 & Severe & [Specific adjustment - e.g., Reduce 50\% or avoid] \\
+<15 or dialysis & ESRD & [Use with caution or contraindicated] \\
+\bottomrule
+\end{tabular}
+\caption{Dose adjustments for renal impairment}
+\end{table}
+
+\subsection{Hepatic Impairment}
+
+[Similar table for hepatic dose adjustments using Child-Pugh class or bilirubin/transaminases]
+
+\section{Clinical Decision Algorithm}
+
+% Simple flowchart example - can be expanded with more complex TikZ
+\begin{center}
+\begin{tikzpicture}[node distance=1.8cm, auto,
+  decision/.style={diamond, draw, fill=conditionalyellow!30, text width=4.5em, text centered, inner sep=1pt, font=\tiny},
+  process/.style={rectangle, draw, fill=stronggreen!20, text width=5.5em, text centered, rounded corners, minimum height=2em, font=\tiny},
+  terminal/.style={rectangle, draw, fill=highlightgray, text width=5.5em, text centered, rounded corners=6pt, minimum height=2em, font=\tiny},
+  alert/.style={rectangle, draw=warningred, line width=1pt, fill=warningred!10, text width=5.5em, text centered, rounded corners, minimum height=2em, font=\tiny\bfseries},
+  arrow/.style={thick,->,>=stealth}]
+
+  \node [terminal] (start) {[Disease] Diagnosis Confirmed};
+  \node [decision, below of=start, node distance=1.8cm] (biomarker) {Biomarker\\ Positive?};
+  \node [process, left of=biomarker, node distance=3.5cm] (optionA) {Targeted\\ Therapy};
+  \node [process, right of=biomarker, node distance=3.5cm] (optionB) {Standard\\ Therapy};
+  \node [terminal, below of=biomarker, node distance=2.5cm] (monitor) {Monitor Response\\ Every X weeks};
+  
+  \draw [arrow] (start) -- (biomarker);
+  \draw [arrow] (biomarker) -- node[above] {Yes} (optionA);
+  \draw [arrow] (biomarker) -- node[above] {No} (optionB);
+  \draw [arrow] (optionA) |- (monitor);
+  \draw [arrow] (optionB) |- (monitor);
+\end{tikzpicture}
+\end{center}
+
+{\footnotesize \textit{Figure 1: Simplified treatment selection algorithm. See detailed algorithm in references for complete decision pathway.}}
+
+\section{Monitoring Protocol}
+
+\subsection{On-Treatment Monitoring}
+
+\begin{table}[H]
+\centering
+\footnotesize
+\begin{tabular}{lccl}
+\toprule
+\textbf{Assessment} & \textbf{Baseline} & \textbf{Frequency} & \textbf{Rationale} \\
+\midrule
+CBC with differential & $\checkmark$ & Before each cycle & Myelosuppression \\
+Comprehensive metabolic panel & $\checkmark$ & Before each cycle & Organ function \\
+[Specific biomarker] & $\checkmark$ & Every X cycles & [Reason] \\
+Imaging (CT chest/abd/pelvis) & $\checkmark$ & Every X weeks & Response assessment \\
+ECOG performance status & $\checkmark$ & Every visit & Functional status \\
+Toxicity assessment (CTCAE) & - & Every visit & Safety monitoring \\
+\bottomrule
+\end{tabular}
+\caption{Recommended monitoring schedule}
+\end{table}
+
+\subsection{Dose Modification Guidelines}
+
+\textbf{Hematologic Toxicity}:
+\begin{itemize}
+\item \textbf{ANC <1.0 or Platelets <75k}: Delay treatment, recheck weekly, dose reduce 20\% when recovered
+\item \textbf{ANC <0.5 or Platelets <50k}: Hold treatment, G-CSF support, dose reduce 25-40\%
+\item \textbf{Febrile neutropenia}: Hold, hospitalize, antibiotics, dose reduce 25\% when recovered
+\end{itemize}
+
+\textbf{Non-Hematologic Toxicity}:
+\begin{itemize}
+\item \textbf{Grade 2}: Continue with supportive care, consider dose modification if persistent
+\item \textbf{Grade 3}: Hold until $\leq$Grade 1, resume at reduced dose (20-25\% reduction)
+\item \textbf{Grade 4}: Discontinue treatment or hold pending recovery (case-by-case)
+\end{itemize}
+
+\textbf{Specific Toxicity Management}:
+\begin{itemize}
+\item \textbf{[Specific AE]}: [Management approach - e.g., Diarrhea Grade 3: Hold treatment, loperamide, hydration, resume at reduced dose when $\leq$Grade 1]
+\item \textbf{[Immune-related AE]}: [Management - e.g., Pneumonitis Grade 2+: Hold immunotherapy, corticosteroids, pulmonology consultation]
+\end{itemize}
+
+\section{Treatment Recommendations by Clinical Scenario}
+
+\subsection{Scenario 1: [Specific Clinical Situation]}
+
+\begin{tcolorbox}[enhanced,colback=stronggreen!10,colframe=stronggreen,
+title={\textbf{RECOMMENDATION} \hfill \textbf{GRADE: 1A}},
+fonttitle=\bfseries\small,coltitle=black]
+{\small
+\textbf{We recommend} [specific intervention] for [patient population].
+
+\textbf{Evidence}:
+\begin{itemize}
+\item [Primary supporting evidence with results]
+\item [Guideline concordance - NCCN, ASCO, ESMO]
+\end{itemize}
+
+\textbf{Benefits}: [Quantified improvements - e.g., 8.7-month PFS benefit, HR 0.46]
+
+\textbf{Harms}: [Quantified risks - e.g., 15\% grade 3-4 immune-related AEs]
+
+\textbf{Balance}: Benefits clearly outweigh harms for most patients
+}
+\end{tcolorbox}
+
+\subsection{Scenario 2: [Alternative Clinical Situation]}
+
+\begin{tcolorbox}[enhanced,colback=conditionalyellow!10,colframe=conditionalyellow,
+title={\textbf{RECOMMENDATION} \hfill \textbf{GRADE: 2B}},
+fonttitle=\bfseries\small,coltitle=black]
+{\small
+\textbf{We suggest} [intervention] for [patient population] who value [specific outcome].
+
+\textbf{Evidence}: [Moderate-quality evidence summary]
+
+\textbf{Trade-offs}:
+\begin{itemize}
+\item \textbf{Advantages}: [e.g., Oral administration, less frequent monitoring]
+\item \textbf{Disadvantages}: [e.g., Lower response rate, more out-of-pocket cost]
+\end{itemize}
+
+\textbf{Patient Values}: Substantial variability in how patients value outcomes; shared decision-making essential
+}
+\end{tcolorbox}
+
+\section{Alternative Approaches}
+
+\subsection{Non-Recommended Options}
+
+\begin{tcolorbox}[enhanced,colback=warningred!10,colframe=warningred,
+title={\textbf{NOT RECOMMENDED}},
+fonttitle=\bfseries\small,coltitle=white,colbacktitle=warningred]
+{\small
+\textbf{[Intervention X]} is \textbf{not recommended} for [population].
+
+\textbf{Reason}: [Evidence of harm, lack of benefit, or superior alternatives available]
+
+\textbf{Evidence}: [Supporting data showing no benefit or harm]
+}
+\end{tcolorbox}
+
+\section{Supportive Care}
+
+\subsection{Symptom Management}
+
+\begin{itemize}
+\item \textbf{Pain Control}: [Analgesic recommendations, WHO ladder]
+\item \textbf{Nausea Prevention}: [Antiemetics - e.g., 5-HT3 antagonists, NK1 antagonists for highly emetogenic]
+\item \textbf{Bone Health}: [e.g., Bisphosphonates or denosumab if bone metastases]
+\item \textbf{Nutritional Support}: [Consult if weight loss >5\%, cachexia management]
+\item \textbf{Psychosocial Support}: [Depression screening, support groups, palliative care early integration]
+\end{itemize}
+
+\subsection{Growth Factor Support}
+
+\textbf{G-CSF Prophylaxis}:
+\begin{itemize}
+\item \textbf{Primary prophylaxis}: If febrile neutropenia risk $\geq$20\%
+\item \textbf{Secondary prophylaxis}: After prior febrile neutropenia episode
+\item Agent: [Pegfilgrastim 6 mg SC day 2 or filgrastim 5 mcg/kg SC daily days 3-10]
+\end{itemize}
+
+\section{Follow-Up and Surveillance}
+
+\subsection{During Active Treatment}
+
+[Schedule outlined in Monitoring Protocol section above]
+
+\subsection{Post-Treatment Surveillance}
+
+\begin{table}[H]
+\centering
+\footnotesize
+\begin{tabular}{lccc}
+\toprule
+\textbf{Time Period} & \textbf{Imaging} & \textbf{Labs} & \textbf{Clinical Visits} \\
+\midrule
+Year 1 & Every 3 months & Every 3 months & Every 3 months \\
+Year 2 & Every 3-4 months & Every 3-4 months & Every 3-4 months \\
+Years 3-5 & Every 6 months & Every 6 months & Every 6 months \\
+Year 5+ & Annually & Annually & Annually \\
+\bottomrule
+\end{tabular}
+\caption{Post-treatment surveillance schedule (adjust based on risk of recurrence)}
+\end{table}
+
+\section{Clinical Trial Opportunities}
+
+\textbf{When to Consider Clinical Trials}:
+\begin{itemize}
+\item After progression on standard therapies
+\item High-risk disease with poor prognosis on standard therapy
+\item Novel biomarker potentially predictive of response
+\item Patient preference for investigational approach
+\end{itemize}
+
+\textbf{Resources}:
+\begin{itemize}
+\item ClinicalTrials.gov search: [Specific keywords]
+\item [Institution] clinical trials office: [Contact information]
+\end{itemize}
+
+\section{Shared Decision-Making}
+
+\subsection{Key Discussion Points}
+
+\textbf{Goals of Care}:
+\begin{itemize}
+\item Curative intent vs prolonged disease control vs palliation
+\item Quality of life vs quantity of life trade-offs
+\item Functional independence goals
+\end{itemize}
+
+\textbf{Treatment Options Counseling}:
+\begin{itemize}
+\item Expected benefits (median survival, response rates)
+\item Potential harms (toxicity profile, quality of life impact)
+\item Treatment schedule and logistics (frequency of visits, IV vs oral)
+\item Financial considerations (out-of-pocket costs, time off work)
+\end{itemize}
+
+\textbf{Decision Aids}:
+\begin{itemize}
+\item Number Needed to Treat: [e.g., Treat X patients to prevent 1 progression event]
+\item Survival benefit visualization: [X-month improvement in median survival]
+\end{itemize}
+
+\section{References}
+
+\begin{enumerate}
+\item [Primary clinical trial reference]
+\item [Secondary supporting trial]
+\item [NCCN Guidelines, version]
+\item [ASCO/ESMO Guideline reference]
+\item [Meta-analysis or systematic review if applicable]
+\item [Biomarker validation reference]
+\end{enumerate}
+
+\vspace{10pt}
+
+\hrule
+\vspace{4pt}
+{\footnotesize
+\textbf{Guideline Development Committee}:\\
+[Names and titles of committee members, affiliations]
+
+\textbf{Evidence Review Date}: [Date]\\
+\textbf{Guideline Effective Date}: [Date]\\
+\textbf{Next Scheduled Review}: [Date] (or earlier if practice-changing evidence published)
+
+\textbf{Conflicts of Interest}: [None / See disclosure statements]
+
+\textbf{Methodology}: GRADE framework for evidence evaluation and recommendation development. Systematic literature review conducted [date range]. Guidelines concordance checked with NCCN, ASCO, ESMO current versions.
+
+\textbf{For Questions}: Contact [Name], [Title] at [Email/Phone]
+}
+
+\end{document}
+

package/skills/clinical-decision-support/references/README.md

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+# Clinical Decision Support Skill
+
+Professional clinical decision support documents for medical professionals in pharmaceutical and clinical research settings.
+
+## Quick Start
+
+This skill enables generation of three types of clinical documents:
+
+1. **Individual Patient Treatment Plans** - Personalized protocols for specific patients
+2. **Patient Cohort Analysis** - Biomarker-stratified group analyses with outcomes
+3. **Treatment Recommendation Reports** - Evidence-based clinical guidelines
+
+All documents are generated as compact, professional LaTeX/PDF files.
+
+## Directory Structure
+
+```
+clinical-decision-support/
+├── SKILL.md                     # Main skill definition
+├── README.md                    # This file
+│
+├── references/                  # Clinical guidance documents
+│   ├── patient_cohort_analysis.md
+│   ├── treatment_recommendations.md
+│   ├── clinical_decision_algorithms.md
+│   ├── biomarker_classification.md
+│   ├── outcome_analysis.md
+│   └── evidence_synthesis.md
+│
+├── assets/                      # Templates and examples
+│   ├── cohort_analysis_template.tex
+│   ├── treatment_recommendation_template.tex
+│   ├── clinical_pathway_template.tex
+│   ├── biomarker_report_template.tex
+│   ├── example_gbm_cohort.md
+│   ├── recommendation_strength_guide.md
+│   └── color_schemes.tex
+│
+└── scripts/                     # Analysis and generation tools
+    ├── generate_survival_analysis.py
+    ├── create_cohort_tables.py
+    ├── build_decision_tree.py
+    ├── biomarker_classifier.py
+    └── validate_cds_document.py
+```
+
+## Example Use Cases
+
+### Create a 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 Treatment Recommendations
+```
+> Create evidence-based treatment recommendations for HER2-positive 
+  metastatic breast cancer with GRADE methodology
+```
+
+### Build Clinical Pathway
+```
+> Generate a clinical decision algorithm for acute chest pain 
+  management with TIMI risk score
+```
+
+## Key Features
+
+- **GRADE Methodology**: Evidence quality grading (High/Moderate/Low/Very Low)
+- **Recommendation Strength**: Strong (Grade 1) vs Conditional (Grade 2)
+- **Biomarker Integration**: Genomic, expression, and molecular subtype classification
+- **Statistical Analysis**: Kaplan-Meier, Cox regression, log-rank tests
+- **Guideline Concordance**: NCCN, ASCO, ESMO, AHA/ACC integration
+- **Professional Output**: 0.5in margins, color-coded boxes, publication-ready
+
+## Dependencies
+
+Python scripts require:
+- `pandas`, `numpy`, `scipy`: Data analysis and statistics
+- `lifelines`: Survival analysis (Kaplan-Meier, Cox regression)
+- `matplotlib`: Visualization
+- `pyyaml` (optional): YAML input for decision trees
+
+Install with:
+```bash
+pip install pandas numpy scipy lifelines matplotlib pyyaml
+```
+
+## References Included
+
+1. **Patient Cohort Analysis**: Stratification methods, biomarker correlations, statistical comparisons
+2. **Treatment Recommendations**: Evidence grading, treatment sequencing, special populations
+3. **Clinical Decision Algorithms**: Risk scores, decision trees, TikZ flowcharts
+4. **Biomarker Classification**: Genomic alterations, molecular subtypes, companion diagnostics
+5. **Outcome Analysis**: Survival methods, response criteria (RECIST), effect sizes
+6. **Evidence Synthesis**: Guideline integration, systematic reviews, meta-analysis
+
+## Templates Provided
+
+1. **Cohort Analysis**: Demographics table, biomarker profile, outcomes, statistics, recommendations
+2. **Treatment Recommendations**: Evidence review, GRADE-graded options, monitoring, decision algorithm
+3. **Clinical Pathway**: TikZ flowchart with risk stratification and urgency-coded actions
+4. **Biomarker Report**: Genomic profiling with tier-based actionability and therapy matching
+
+## Scripts Included
+
+1. **`generate_survival_analysis.py`**: Create Kaplan-Meier curves with hazard ratios
+2. **`create_cohort_tables.py`**: Generate baseline, efficacy, and safety tables
+3. **`build_decision_tree.py`**: Convert text/JSON to TikZ flowcharts
+4. **`biomarker_classifier.py`**: Stratify patients by PD-L1, HER2, molecular subtypes
+5. **`validate_cds_document.py`**: Quality checks for completeness and compliance
+
+## Integration
+
+Integrates with existing skills:
+- **scientific-writing**: Citation management, statistical reporting
+- **clinical-reports**: Medical terminology, HIPAA compliance
+- **scientific-schematics**: TikZ flowcharts
+
+## Version
+
+Version 1.0 - Initial release
+Created: November 2024
+Last Updated: November 5, 2024
+
+## Questions or Feedback
+
+This skill was designed for pharmaceutical and clinical research professionals creating clinical decision support documents. For questions about usage or suggestions for improvements, contact the Scientific Writer development team.
+