medical-research-skills

Use when identifying seminal papers in a research field, mapping research lineage and intellectual heritage, discovering related work through reference tracking, or finding potential collaborators through co-citation analysis. Maps citation networks to trace research evolution...

Use when formatting references for journal submission, converting between citation styles (APA, MLA, Vancouver, Chicago), generating bibliographies for manuscripts, or ensuring consistent reference formatting. Automatically formats citations and bibliographies in 1000+ academi...

Comprehensive citation management for academic research; use when you need to discover papers (Google Scholar/PubMed), extract/verify metadata (DOI/PMID/arXiv/URL), and produce validated, clean BibTeX for manuscripts.

Build and visualize a citation network from a source/target CSV to identify key papers, communities, and emerging hotspots; use when you have citation pairs and need fast literature review or trend analysis.

Calibrates manuscript claim strength so wording matches the actual evidence level, study design, and validation status.

Designs retrospective or prospective clinical cohort study protocols for biomedical and clinical research. Always use this skill when the user needs a cohort-based study plan rather than a general study idea, evidence summary, or mechanistic experiment design. Focus on cohort appropriateness, enrollment logic, baseline time-zero definition, follow-up structure, endpoint definition, variable collection, confounding control, and a coherent primary statistical analysis line. Do not invent data availability, follow-up completeness, outcome ascertainment quality, sample size adequacy, or causal interpretability.

Use when cleaning clinical trial data, preparing data for FDA/EMA submission, standardizing SDTM datasets, handling missing values in clinical studies, detecting outliers in lab results, or converting raw CRF data to CDISC format. Cleans and standardizes clinical trial data fo...

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). ...

Identify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application. For diagnostic reasoning, treatment decisions, and

Clarifies a vague clinical or biomedical research idea into a structured, bounded, searchable, researchable, and testable question. Always use this skill whenever a user has an early-stage clinical or research thought, an over-broad topic, an ill-defined evidence question, or an unclear problem statement that must be translated into a question framing suitable for literature retrieval, evidence synthesis, gap analysis, study design, or downstream protocol planning. Never jump straight to answering the substantive medical question unless the user explicitly asks for that. Focus first on question framing, boundary setting, and downstream-ready formulation.

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory complianc...

Batch extracts and verifies structured information (PMID, title, abstract, methodology, results, etc.) from clinical research literature using PMIDs. Use when the user wants to extract details from specific PMIDs.

Find clinical trials for a gene, variant, or condition from ClinicalTrials.gov + EUCTR, with FHIR R4 output

Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for [intervention]", or when developi...

Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.

Query the ClinicalTrials.gov API v2 to search for clinical trials, retrieve detailed study protocols, and analyze recruitment status; use when you need to find trials by condition/drug, export results, or verify study details by NCT ID.

Monitor and summarize competitor clinical trial status changes from ClinicalTrials.gov.

Generates a structured prompt framework for clinical study protocols. Supports Diagnostic, Efficacy, Etiology, and Prognosis studies. Calculates sample size and provides logic guides for LLMs.

Unified tool for calculating sample sizes for Diagnostic, Efficacy, Etiology, and Prognosis clinical studies. Supports various statistical methods (Sensitivity/Specificity, Log-rank, Chi-square, EPV, etc.).

Access ClinPGx pharmacogenomics data (successor to PharmGKB) when you need to query gene-drug interactions, CPIC guidelines, allele functions, and drug-label PGx content for precision medicine and genotype-guided dosing.

Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF files with ClinVar annotations.

Detect copy number variations from whole genome sequencing data and generate publication-quality genome-wide CNV plots. Supports CNV calling, segmentation, and visualization for cancer genomics and rare disease analysis.

Constraint-based reconstruction and analysis (COBRA) for metabolic models; use when you need to simulate growth/production, analyze flux ranges, or run knockout and medium studies from SBML/JSON/YAML models.

Use when refactoring research code for publication, adding documentation to existing analysis scripts, creating reproducible computational workflows, or preparing code for sharing with collaborators. Transforms research code into publication-ready, reproducible workflows. Adds documentation, implements error handling, creates environment specifications, and ensures computational reproducibility for scientific publications.

Evaluates the quality of cohort studies using the Newcastle-Ottawa Scale (NOS). Use when the user provides a cohort study article or text and needs a quality assessment report.