aipoch/medical-research-skills
59 skills · 27 total installs
$npx skills add aipoch/medical-research-skillsSkillInstalls
XGBoost-analysisUse when building XGBoost models on tabular data and returning feature importance ranking outputs.author-response-builderTurns reviewer comments into structured, professional point-by-point responses linked to manuscript revisions, clarifications, rebuttals, and additional…medical-english-precision-editorImproves medical English precision without changing the underlying facts, evidence boundaries, or intended scientific meaning.methods-section-writerTurns your protocol and analysis workflow into publication-ready Methods text.reference-integrity-checkerChecks whether manuscript references are accurately matched to claims, appropriately scoped, and not overextended, misquoted, or second-hand cited.reporting-guideline-compliance-checkerChecks biomedical manuscripts against reporting guidelines such as CONSORT, STROBE, PRISMA, and TRIPOD to identify missing or weak reporting elements before…results-section-structurerOrganizes biomedical figures, analyses, and result blocks into a clear Results section structure with disciplined narrative ordering and evidence-aware…table-narrative-writerConverts biomedical table content into clear manuscript or presentation narrative by prioritizing meaningful patterns, contrasts, and interpretation boundaries…title-and-abstract-optimizerOptimizes manuscript titles and abstracts for information density, factual accuracy, and submission fit in biomedical research writing.claim-strength-calibratorCalibrates manuscript claim strength so wording matches the actual evidence level, study design, and validation status.discussion-composerComposes a Discussion around key findings, mechanisms, clinical relevance, and limitations.figure-legend-writerWrites complete, publication-grade figure legends that can stand on their own.introduction-section-writerWrites the full Introduction section of a biomedical manuscript based on an approved or sufficiently clear study logic, while preserving evidence boundaries…limitation-and-risk-writerAcknowledges limitations in sample, design, measurement, and validation in a professional way that improves credibility without undermining the whole paper.paper-sprint-reviewScrum-inspired paper review, revision, and R&R workflow. Handles docx/tex/md/PDF in English or Chinese.results-section-writerWrites the full Results section of a biomedical manuscript from a sufficiently clear result structure, figure inventory, or analysis summary while preserving…revision-strategy-plannerBuilds prioritized manuscript revision plans for major or minor revisions by separating comments that require experiments, analyses, clarification,…target-journal-matcherMatches your study to appropriate journals based on topic, design, and evidence strength.LightGBM-analysisUse when training a LightGBM model on tabular data in R and returning model metrics, feature importance ranking tables, and feature importance plots.arxiv-preflightRun a submission-readiness preflight on a manuscript before arXiv upload.batch-effect-correctionUse when correcting batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and…cerna-analysisUse when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports…cibersort-immune-infiltration-analysisUse when estimating relative immune cell infiltration from a bulk expression matrix with a CIBERSORT-style nu-SVR deconvolution workflow based on an LM22…conference-abstract-writerCondenses a full study into conference-submission abstract format.consensus-clustering-analysisUse when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus…consistency-checker-across-manuscriptChecks consistency across title, abstract, methods, results, figures, tables, and supplements to identify internal contradictions and version drift in…cover-letter-drafterDrafts journal-ready cover letters for manuscript submission. Use when preparing a submission package, communicating the manuscript's contributions and journal…decision-curve-analysisUse when evaluating the clinical utility of a binary prediction model from a single clinical CSV file by fitting a logistic decision-curve model, plotting…decision-tree-analysisUse when building a decision tree model in R and generating feature importance ranking outputs.deg-screening-analysisUse when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a…differential-expression-analysisUse when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with…elastic-net-feature-selectionUse when selecting predictive genes or other molecular features from bulk expression matrices for binary case-vs-control classification with elastic net…estimate-immune-score-analysisUse this skill to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally…external-model-validationUse when validating an existing prognostic risk signature on an external bulk expression cohort with survival outcomes, producing risk scores, Kaplan-Meier…gene-protein-expression-matrix-normalizationUse when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization…gokeggUse when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart.grant-specific-aims-writerWrites Specific Aims pages for grant applications. Use when drafting or revising the Specific Aims page (NIH R01/R21/R03), NSF Project Summary, or equivalent…graphical-abstract-generatorConverts a biomedical study storyline into a graphical abstract and, when direct image capability is available, generates the graphical abstract directly;…gseaRun GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.gsva-analysis-and-visualizationUse this skill to run GSVA or ssGSEA pathway-level differential analysis from a bulk expression matrix and a sample group file, then generate a heatmap from…hierarchical-clustering-plotUse when building a sample-level hierarchical clustering dendrogram from a bulk expression matrix and sample annotation table, especially for QC, batch…immune-pathway-analysisRun 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…introduction-logic-builderBuilds background-gap-objective logic for biomedical manuscript introductions with clear study positioning and disciplined narrative structure.km-survival-curveUse when generating Kaplan-Meier survival curves from tabular survival data containing time, event status, and a precomputed risk group.knn-imputationUse when filtering genes with high missingness and then imputing missing values in a bulk expression matrix with group-aware KNN through DMwR2, where donor…lasso-logistics-analysisUse when building a binary classification model from an expression matrix or other omics feature matrix with LASSO logistic regression, cross-validation, and…latex-manuscript-format-converterConverts existing manuscript content into LaTeX format aligned with a target journal, conference, or template while preserving manuscript meaning and…lay-summary-for-cross-disciplinary-teamsRewrites technical research content into a structured lay summary that cross-disciplinary teams can quickly understand and act on.lncrna-regulatory-network-construction-analysisUse this bioinformatics data analysis skill to construct a database-driven lncRNA-mRNA regulatory network from target lncRNA and/or gene lists by projecting…model-calibration-curveUse when assessing how well a survival model's predicted probabilities agree with observed outcomes by fitting a Cox model and generating bootstrap calibration…nomogram-constructionUse when constructing a prognosis nomogram from survival-related clinical predictors, exporting the nomogram bundle and C-index table, and optionally rendering…pca-dimensionality-reductionUse when performing PCA principal component dimensionality reduction on tabular numeric data.poster-storyline-builderReorganizes a paper into a storyline suitable for scientific posters.ppi-network-analysisUse 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…rf-model-importance-analysisUse 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…roc-diagnostic-performanceUse when evaluating diagnostic biomarker performance from case-control expression data with logistic regression and ROC curves, exporting coefficient and AUC…sample-correlation-analysisUse when performing correlation analysis between two variables including Pearson and Spearman correlation methods.sample-group-sankey-plotUse when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk…slide-deck-for-lab-meetingStructures research progress into focused and actionable slides for lab meetings or project reviews without inventing missing content.