aipoch/medical-research-skills - 第 6 页

immune-pathway-analysis

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.

原文语言：英语

km-survival-curve

Use when generating Kaplan-Meier survival curves from tabular survival data containing time, event status, and a precomputed risk group. Supports command-line parameter input, parameter validation, automatic time-unit handling, single-file PDF figure export,…

原文语言：英语

lightgbm-analysis

Use when training a LightGBM model on tabular data in R and returning model metrics, feature importance ranking tables, and feature importance plots.

原文语言：英语

lncrna-regulatory-network-construction-analysis

Use this bioinformatics data analysis skill to construct a database-driven lncRNA-mRNA regulatory network from target lncRNA and/or gene lists by projecting shared miRNA evidence from local ceRNA reference tables. It does not infer networks from expression…

原文语言：英语

pca-dimensionality-reduction

Use when performing PCA principal component dimensionality reduction on tabular numeric data. Supports command-line parameter input, automatic numeric feature selection, parameter validation, result directory creation, and CSV or TXT format result export.

原文语言：英语

ppi-network-analysis

Use when you need a standardized R CLI workflow to build a protein-protein interaction network from a local gene list and an offline STRING cache, export node and edge tables, and render a reproducible PDF network plot. NOT for online API fetching, arbitrary…

原文语言：英语

rf-model-importance-analysis

Use when you need a standardized R CLI workflow to train a two-class random forest model from an expression-like feature matrix, rank variable importance, and generate reproducible error and importance plots. NOT for regression tasks, multi-class…

原文语言：英语

sample-correlation-analysis

Use when performing correlation analysis between two variables including Pearson and Spearman correlation methods. Supports command-line parameter input, automatic data format detection, parameter validation, result directory creation, and CSV or TXT format…

原文语言：英语

ssgsea-immune-infiltration-analysis

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…

原文语言：英语

svm-model-importance-analysis

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,…

原文语言：英语

time-dependent-roc

Use when performing time-dependent ROC curve analysis for survival data with follow-up time, event status, and a numeric marker. Supports CSV/TXT/TSV/Excel input, `risk_score` as the default marker unless `--marker_col` is provided, parameter validation,…

原文语言：英语

wgcna-analysis

Use when building a weighted gene co-expression network from a bulk expression matrix and a sample group file, filtering variable genes by MAD, identifying co-expression modules with WGCNA, correlating modules with traits, and exporting module-level plots and…

原文语言：英语

xgboost-analysis

Use when building XGBoost models on tabular data and returning feature importance ranking outputs. Supports binary classification and regression with automatic task detection, train-test split, performance tables, feature importance ranking tables, and PNG…

原文语言：英语

basic-discovery-translational-opportunity-finder

Finds translational opportunities that connect basic-research discoveries to clinically meaningful use cases such as diagnosis, stratification, prognosis, treatment response prediction, monitoring, or therapeutic development. Use this skill when a user wants…

原文语言：英语

bioinformatics-translational-opportunity-finder

Identifies translationally meaningful paths for bioinformatics findings by mapping omics or computational discoveries to diagnosis, stratification, prognosis, treatment-response, monitoring, or target-nomination use cases, while auditing bridge evidence,…

原文语言：英语

biomarker-landscape-scanner

Scans the biomarker landscape of a disease area by biomarker type, clinical/research use case, evidence layer, validation status, and maturity level. Use this skill when a user wants a field-level biomarker evidence map rather than a generic literature…

原文语言：英语

biomedical-search-strategy-builder

Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases. Use when a user needs to construct a MeSH-based Boolean query, design a systematic review search, expand a concept with synonyms, apply study-type or date…

原文语言：英语

clinical-question-clarifier

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…

原文语言：英语

contradictory-findings-resolver

Explains why studies on the same biomedical topic reach different or opposing conclusions by auditing differences in population, endpoint definition, sample source, assay or platform, study design, statistical model, adjustment strategy, validation chain, and…

原文语言：英语

disease-mechanism-evidence-map

Systematically maps mechanism evidence for a disease from molecules to pathways, cell types, tissues, biological consequences, and clinical phenotypes. Always use this skill when a user needs a layered mechanism evidence chain rather than a flat summary or…

原文语言：英语

drug-target-evidence-landscape

Organizes the evidence and competitive landscape around a drug, target, or pathway by separating disease relevance, tractability, preclinical evidence, clinical evidence, modality fit, and crowding. Always map what is biologically supported, what is…

原文语言：英语

evidence-level-ranker

Ranks papers by evidence family, methodological quality tier, validation depth, and claim discipline; assigns anchor, context-setting, mechanistic support, or caution citation roles; prevents prestige-based or design-label-based ranking errors.

原文语言：英语

high-value-paper-screener

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

原文语言：英语

medical-topic-saturation-and-whitespace-checker

Maps whether a biomedical research topic, subtopic, or study angle is truly saturated, superficially crowded, strategically occupied, or still open for differentiated entry. Use this skill when a user wants to know whether a hot medical research direction is…

原文语言：英语

method-gap-detector

Detects methodological gaps across study design, analysis, validation, bias control, reproducibility, and implementation readiness within a biomedical research area. Use this skill when a user wants to identify what current studies are still methodologically…

原文语言：英语

methods-reverse-engineer

Reverse-engineers the methods section of a biomedical paper into a structured, reproducible workflow. Use this skill when a user wants to understand how a study was actually executed, extract data sources, inclusion/exclusion logic, preprocessing, analytical…

原文语言：英语

multi-database-literature-collector

Collects candidate biomedical literature across multiple databases, adapts search logic by database, preserves source metadata, and organizes results into a structured, screening-ready candidate pool. Always use this skill when a user wants cross-database…

原文语言：英语

novelty-vs-feasibility-assessor

Assesses whether a medical research topic is worth starting now by separating true novelty from pseudo-novelty, auditing real feasibility under stated resource constraints, and forcing a concrete start / narrow / redesign / stop decision. Always require…

原文语言：英语

paper-to-claim-verifier

Verifies whether a scientific or biomedical claim is actually supported by the cited original papers rather than by citation drift, overstatement, selective citation, or correlation-to-causation inflation. Use this skill whenever a user wants to check whether…

原文语言：英语

population-gap-detector

Detects overlooked, underrepresented, weakly resolved, or poorly validated populations and subgroups within a biomedical research area so users can identify more precise and meaningful study populations. Always use this skill when the real question is not…

原文语言：英语

preprint-surveillance-finder

Tracks the latest preprints and emerging research topics related to your topic across bioRxiv, medRxiv, and arXiv. Use when a user wants to discover what is being published right now before it reaches journals, monitor competitor directions, spot new…

原文语言：英语

result-reliability-checker

Assesses whether study results are trustworthy by auditing design integrity, sample structure, statistical handling, bias control, validation chain, and claim discipline. It identifies where results are robust, fragile, overfit, under-validated, or…

原文语言：英语

study-design-identifier

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,…

原文语言：英语

topic-evidence-mapper

Rapidly maps the evidence landscape around a medical topic by organizing major research streams, target populations, endpoints, methods, evidence density, and thin areas. Use this skill BEFORE medical-research-gap-finder — it provides the structured landscape…

原文语言：英语

unmet-clinical-need-extractor

Extracts concrete unmet clinical needs from guidelines, reviews, real-world studies, and clinical-practice evidence. Use this skill when a user wants to turn broad medical research value into specific clinical pain points such as weak early detection, poor…

原文语言：英语

mendel

Gregor Mendel — genetics mentor, patient experimenter, and gardener-monk. Trigger this skill when users ask about genetics, heredity, inheritance patterns, Mendelian laws, dominant/recessive traits, gene segregation, independent assortment, Punnett squares,…

原文语言：英语

active-comparator-single-soc-faers-safety-comparison

Generates complete FAERS pharmacovigilance study designs for multi-drug or class-level safety comparison inside one predefined SOC or AE family using active comparators, disproportionality analysis, subgroup characterization, and reviewer-facing evidence…

原文语言：英语

aim-and-hypothesis-designer

Designs primary aims, secondary aims, and testable hypotheses from broad biomedical research ideas. Use this skill when a user needs to convert a loose study idea into a tighter protocol-framing structure with clear aim hierarchy, hypothesis discipline, and…

原文语言：英语

animal-and-cell-validation-planner

Designs cell-based and animal-based validation plans that translate computational, omics, biomarker, genetic, or clinical findings into experimentally testable validation routes. Always use this skill whenever a user wants to move from an in silico,…

原文语言：英语

bidirectional-multi-phenotype-mr-research-planner

Generates complete bidirectional multi-phenotype Mendelian randomization research designs from a user-provided exposure family and outcome family. Always use this skill whenever a user wants to design, plan, or build a genome-wide causal-inference study based…

原文语言：英语