medical-research-skills

Compare experimental method details between two Zotero PDF papers, identify protocol differences (ratios, dosages, timing, conditions), search supporting literature to explain why they differ, and generate an HTML report. Use when you need a parameter-level comparison of two methods and evidence-backed reasons for discrepancies.

Generates a full expert interview article including introduction, Q&A body, and summary based on interview questions and expert background. Use when you have interview questions and an expert profile and need a polished article.

Generates professional interview titles and questions based on expert background and topic. Provides a structured workflow for interview preparation.

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generate...

Use when validating an existing prognostic risk signature on an external bulk expression cohort with survival outcomes, producing risk scores, Kaplan-Meier curves, risk distribution plots, heatmap, and time-dependent ROC curves. NOT for: model training, feature selection, nomogram construction, calibration analysis, or single-cell data.

Use facs gating viz style for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

Generates complete FAERS-based multi-drug single-SOC safety comparison research designs from a user-provided drug set, comparator, and adverse event domain. Always use this skill when users want to compare safety signals across multiple drugs using FAERS or OpenFDA data within one System Organ Class (SOC) or bounded AE domain. Trigger for:"FAERS study comparing drugs within one SOC", "publishable FAERS safety comparison paper", "compare neuropsychiatric adverse events across beta-blockers", "Lite/Standard/Advanced FAERS safety plans", "active-comparator restricted disproportionality", "adjusted ROR logistic regression FAERS", "within-class head-to-head drug comparison", "pharmacovigilance signal comparison", "single-SOC PT-level FAERS design", or any phrasing like "I want to compare drug X and drug Y for adverse events in FAERS" or "build a comparative pharmacovigilance paper". Always output four workload configurations (Lite / Standard / Advanced / Publication+) with a recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, and publication upgrade path.

Generates complete FAERS-style pharmacovigilance disproportionality research designs from a user-provided drug class, comparator strategy, adverse-event domain, and patient-group stratification. Always use this skill whenever a user wants to design, plan, or build a spontaneous-report safety signal study using FAERS or a similar pharmacovigilance database, especially when the article logic includes product selection, indication-group stratification, MedDRA-based adverse-event extraction, serious-case filtering, suspect-drug and concomitant-exclusion logic, reporting odds ratio analysis, comparator-drug benchmarking, cross-drug comparison, and cautious signal interpretation without causal overclaiming. Covers five study patterns (single-drug disproportionality workflow, multi-drug class comparison workflow, indication-stratified workflow, comparator-controlled signal screening workflow...

Generates FAQ lists from complex medical policies or protocols. Trigger when user provides medical documents, policies, or protocols and requests FAQ generation, patient education materials, or simplified explanations.

Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.

Query the openFDA API to retrieve FDA regulatory datasets (drugs, devices, adverse events, recalls, submissions, UNII) when you need programmatic safety/regulatory evidence for analysis or research.

Search FDA industry guidelines by therapeutic area or topic.

Designs a realistic, execution-aware biomedical study version under explicit constraints of samples, time, budget, data access, lab capacity, team skill, and validation resources. Always use this skill when the user has a real study idea, a candidate route, or a partially framed project but cannot assume ideal conditions. If critical feasibility inputs are missing, first clarify what resources are currently available, what resources may be obtainable, and what resources are realistically unavailable. Do not invent access, capabilities, collaborations, or validation resources. Focus first on feasibility-constrained study framing, route narrowing, dependency control, and minimum viable study design.

Reads a paper figure by figure before re-integrating the full narrative, so the user can identify the core findings quickly and check whether each visual actually supports the authors' main claims. Always separate figure content, figure-linked claim, evidentiary strength, and unsupported interpretation. Never fabricate references, PMIDs, DOIs, figure content, panel labels, result values, or study details that were not actually provided.

Generate standardized figure legends for scientific figures and charts; use when preparing publication-ready legends that summarize design, variables, sample size, and key statistical notes.

Writes complete, publication-grade figure legends that can stand on their own. Use when writing or revising figure legends for any scientific figure — bar charts, line graphs, scatter plots, box plots, heatmaps, survival curves, flow cytometry plots, western blots, microscopy images, or schematic diagrams. Also triggers on "write a figure legend for", "help me describe this figure", "my figure needs a legend", "write Figure 1 legend", or "what should a figure legend include".

Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

Organize, back up, compress, split, and merge files/folders using rule-driven plans; use when you need safe previews, conflict handling, and verification before executing file operations.

Perform fast file name and content searches with ripgrep (rg); use it when you need to locate files by glob/regex, find keywords across directories, or replace common find/grep workflows.

Encrypt/decrypt local files, redact sensitive information in documents, and validate password strength when handling private data or preparing files for sharing.

Automatically find references for academic paper Markdown files. Reads full paper text, identifies each knowledge point requiring citation (epidemiological data, mechanism descriptions, existing research conclusions, etc.), searches PubMed for 3-5 most relevant articles per kn...

Parse Flow Cytometry Standard (FCS) files v2.0–3.1 and extract events/metadata for preprocessing workflows (e.g., when you need NumPy arrays, channel info, or CSV/DataFrame export from cytometry files).

Analyze data with `forest-plot-styler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.