medical-research-skills

Use when estimating immune infiltration from bulk RNA-seq expression matrices with ssGSEA/GSVA, comparing case versus control groups, and generating downstream immune-score visualizations. NOT for single-cell RNA-seq, absolute cell proportion estimation, or clinical decision making.

Guided statistical analysis for test selection, assumption checks, power analysis, and APA-style reporting. Use when you need to choose an appropriate statistical test for your data and produce publication-ready results (including effect sizes and diagnostics).

Recommends appropriate statistical methods (T-test vs ANOVA, etc.) based.

Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.

Identifies the real underlying study design used in a medical or biomedical paper, distinguishes primary and secondary design components when papers are hybrid, and converts the paper into an evidence-aware design label suitable for literature appraisal, evidence grading, and downstream review workflows. Always identify the actual design from what the study did, not from how the authors describe it. Never fabricate references, metadata, or study features.

Determines the appropriate Risk of Bias assessment scale for a medical study based on its design (RCT, Cohort, etc.), using PubMed metadata lookup or text analysis. Use when the user wants to know which quality assessment tool to use for a specific paper (given PMID or abstract).

Use study limitations drafter for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

Refines broad, vague, or aspirational biomedical research objectives into clear, bounded, measurable, executable, and downstream-ready study objective statements. Always use this skill when a user has a general aim such as “explore a mechanism,” “study prognosis,” “investigate biomarkers,” or “look at treatment response,” but the objective is still too broad, non-operational, or too ambiguous to support protocol framing, design selection, analysis planning, or hypothesis design. Never assume that polished wording alone means the objective is actionable. Focus first on objective type, missing operational elements, scope discipline, and downstream-ready formulation.

Rewrite drafts according to target writing style or target journal format. Triggers when user says "rewrite in XX style", "match this tone", "format for XX journal", "rewrite following this format". Input can be .docx / .md / .txt or conversation text.

Kaplan-Meier survival analysis tool for clinical and biological research. Generates publication-ready survival curves with statistical tests.

Analyze data with `survival-curve-risk-table` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

Use when you need a standardized R CLI workflow to run two-class SVM-RFE feature ranking on an expression-like matrix, choose an informative feature count from cross-validated error, and generate reproducible ranking and error plots. NOT for regression, multi-class classification, missing-value imputation, or remote data fetching.

Suggest triage levels (Emergency, Urgent, Outpatient) based on red flag symptoms using a rule-based engine. For AI-assisted decision support only — not a substitute for professional medical diagnosis.

Orchestrates a systematic review and meta-analysis workflow following PRISMA 2020 guidelines, from protocol development through multi-database search, screening, data extraction, and evidence synthesis. Use when conducting evidence-based reviews, meta-analyses, or scoping revi...

Automated abstract screening tool for systematic literature reviews with PRISMA workflow support.

Automated generation of baseline characteristics tables (Table 1) for clinical research papers.

Generate publication-ready baseline characteristics tables (Table 1) for clinical research papers with automatic variable type detection, appropriate statistics (mean±SD, median[IQR, n(%)), group comparisons (t-test, chi-square), and APA formatting.

Converts biomedical table content into clear manuscript or presentation narrative by prioritizing meaningful patterns, contrasts, and interpretation boundaries rather than restating every number.

Matches your study to appropriate journals based on topic, design, and evidence strength. Use when deciding where to submit a manuscript, comparing journal options by impact factor vs scope fit vs method tolerance, or finding a realistic submission target after a rejection. Also triggers on "where should I submit this paper", "which journal is best for my study", "find journals for my manuscript", "is this a good fit for [journal]", or "I need a journal with IF around X".

Score the novelty of biological targets through literature mining and.