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, and session metadata capture.

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.

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.

Use 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 the saved GSVA result object. Trigger keywords: GSVA, ssGSEA, pathway enrichment, KEGG pathway analysis, MSigDB. NOT for: gene-level differential expression, single-cell analysis, methylation analysis, clinical diagnosis.

Run GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.

Use 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. NOT for single-cell RNA-seq, methylation data, or non-expression data.

Use when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory analysis. NOT for count-model normalization such as TPM/DESeq2 size factors, batch correction, or single-cell preprocessing.

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.

Language-specific best practices, code quality standards, and framework detection rules. Use when executing refactoring workflows, applying code quality rules, detecting frameworks, or checking language-specific patterns for TypeScript, Python, Go, Swift, or React.

Use this skill to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally generate group-wise ESTIMATE score boxplots plus significance tables when a sample group file is supplied. Trigger keywords: ESTIMATE, immune score, stromal score, tumor microenvironment score. NOT for: immune cell deconvolution, single-cell analysis, differential expression, clinical diagnosis.

This skill should be used when the user asks to "validate plugin structure", "review manifest files", "check frontmatter compliance", "verify tool invocation patterns", "explain plugin component types", or needs Claude Code plugin architectural guidance.

Use when selecting predictive genes or other molecular features from bulk expression matrices for binary case-vs-control classification with elastic net logistic regression, including coefficient path and cross-validation plots. Trigger keywords: elastic net, glmnet, feature selection, binary classification, lambda.min, lambda.1se. NOT for: survival/Cox modeling, multiclass outcomes, single-cell data, or non-expression tables.

Use when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and heatmap visualization. NOT for:single-cell RNA-seq, methylation analysis, non-expression data.

Use when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap. Triggers include DEG analysis, volcano plot, clustered heatmap, limma-based two-group comparison, and case-vs-control screening. NOT for single-cell RNA-seq, multi-group contrasts, count-model workflows such as DESeq2/edgeR, or non-expression omics data.

This skill should be used when the user asks to "understand a codebase", "get code context", "research a library", "explore a repository", "find code examples", "look up documentation", or wants to understand how a specific project or library works before making changes.

Use when building a decision tree model in R and generating feature importance ranking outputs. Supports classification and regression, automatic task detection, parameter validation, model evaluation summaries, and exports of feature-importance tables and figures.

Captures and organizes chaotic brain dumps into a structured, actionable system with zero information loss. Use this skill whenever the user says 'capture this', 'brain dump', 'let me dump some ideas', 'I've got a bunch of thoughts', 'here's everything on my mind', 'idea dump', 'let me get this out of my head', 'I need to organize my thoughts', 'here's what I'm thinking', or any variation where someone is unloading a messy stream of ideas, tasks, thoughts, and plans wanting them turned into something coherent. Also trigger when the user pastes or dictates a long, unstructured block of mixed ideas — even without the exact phrase — the intent is the same. Fast-to-action by design: no upfront intake. Output is four sections (Projects/Ideas, Tasks, Connections, How I Can Help) ending with a directive question. Asks at most one mid-organization clarifying question when a single item is genuinely ambiguous between task and project.

Use 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 and clinical-impact curves, and exporting summary outputs. NOT for: survival calibration, ROC-only discrimination analysis, nomogram construction, or time-to-event outcomes.

SOLID and DRY structure for an Astro `src/` tree — where files live, size limits, and typed props. Use when deciding where new code belongs, adding or splitting an `.astro` page, layout, or component, or placing a service in `src/lib/` or a type in `src/interfaces/`.

Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization. NOT for: differential expression analysis, single-cell clustering workflows, or non-expression tables.