medical-research-skills

Professional beautification tool for gene expression heatmaps, automatically adds clustering trees, color annotation tracks, and intelligently optimizes label layout.

Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata.

Use when building a sample-level hierarchical clustering dendrogram from a bulk expression matrix and sample annotation table, especially for QC, batch inspection, or sample similarity assessment. Trigger keywords: hierarchical clustering, dendrogram, sample QC, batch inspection, sample similarity. NOT for: differential expression testing, gene clustering heatmaps, single-cell clustering workflows.

Quickly judges whether a biomedical paper is worth deep reading by screening for question fit, design quality, sample adequacy, methodological novelty, and reproducibility value.

Clinical-grade PII/PHI detection and de-identification for healthcare text data. Scans all 18 HIPAA identifier categories with confidence scoring, generates audit logs, supports custom regex patterns, and produces de-identified output while preserving document structure.

Evidence-based medical knowledge and research mentor. Trigger this skill when users ask any question related to medicine, clinical science, pharmacology, pathology, epidemiology, or health sciences. Covers: disease mechanisms, drug actions and interactions, differential diagnosis reasoning, clinical guideline interpretation, medical literature appraisal (including GRADE assessment), treatment comparisons, lab and imaging interpretation, public health analysis, and medical terminology. Even if the user doesn't explicitly say "evidence-based" or "medical research," trigger this skill whenever the topic touches health, disease, drugs, or therapeutics. Part of the AIPOCH Medical Research Skill Hub.

Digital pathology image processing toolkit for whole slide images (WSI). Supports WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Access the Human Metabolome Database (HMDB) to search metabolites by name/structure/ID and extract chemical/biological/clinical fields when you need metabolomics research data or automated HMDB XML mining.

Convert HTML files or URLs to high-fidelity PDFs using Puppeteer; auto-detects or forces RTL for Hebrew/Arabic when RTL content is present.

Automated LLM-driven hypothesis generation and testing for tabular datasets; use when you need systematic exploration of empirical patterns (e.g., fraud detection, content analysis) and want to combine literature insights with data-driven hypothesis evaluation.

Structured scientific hypothesis formulation from observations; use when you have experimental observations or preliminary data and need testable hypotheses with predictions, mechanisms, and validation experiments.

Draft IACUC protocol applications with focus on the 3Rs principles justification.

Summarize core safety information from Investigator's Brochures for clinical.

Parse clinical notes and recommend ICD-10-CM diagnosis codes and CPT procedure codes with confidence scoring. Cross-references diagnoses with procedure codes, generates alternatives for medium-confidence matches, and produces structured coding reports with human-review flags.

Replace an ID photo background color (blue/white/red) and/or add a configurable text watermark when you need compliant ID-photo variants from local JPG/PNG files.

Generate renderable, scientific-style SVG graphics directly from natural-language requirements (no image models). Use when users ask for an image/picture/scientific diagram/visualization poster or explicitly request SVG output for web-embeddable vector graphics.

Extract text from images with Tesseract OCR; use it when you need to recognize text from PNG/JPEG/TIFF/BMP images, select a language model, or run OCR via natural-language requests (e.g., "Interpret the image at C:\path\image.png").

Batch-convert and compress local images with Pillow; use when you need an offline, scriptable pipeline for directory-based processing.

Run immune pathway GSVA or ssGSEA analysis from a bulk expression matrix, a sample group file, and a local immune Reactome gene-set table, then export differential pathway results and a heatmap for two-group comparison.

Generate and optimize clinical trial subject inclusion/exclusion criteria to balance scientific rigor with recruitment feasibility.

Builds clear, executable, and auditable inclusion and exclusion criteria for biomedical and clinical research protocols. Always use this skill when a user needs to translate a target population into operational screening rules tied to chart fields, time windows, tests, procedures, prior therapies, exclusions, and reviewable edge cases. Focus on protocol-stage precision, ambiguity reduction, auditability, and screening reproducibility rather than generic study design advice.

Assists researchers in generating INPLASY registration content for meta-analyses from a title and optional protocol. Use when the user wants to draft a INPLASY registration form.

Builds background-gap-objective logic for biomedical manuscript introductions with clear study positioning and disciplined narrative structure.

Writes the full Introduction section of a biomedical manuscript based on an approved or sufficiently clear study logic, while preserving evidence boundaries and introduction discipline.

Assists researchers with Institutional Review Board (IRB) application tasks, including drafting informed consent documents, reviewing research protocols for compliance, generating application forms, and preparing submission checklists. Use when the user mentions IRB, Instituti...