hierarchical-clustering-plot

name

hierarchical-clustering-plot

description

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.

Hierarchical Clustering Plot

When to Use

Use this skill when you need a sample-level hierarchical clustering dendrogram from a bulk expression matrix and a sample annotation table.

• Good fits: sample QC, batch inspection, sample similarity assessment, checking whether annotated sample groups cluster as expected.
• Trigger keywords: hierarchical clustering, dendrogram, sample QC, batch inspection, sample similarity.
• Not for: differential expression testing, gene clustering heatmaps, single-cell clustering workflows.

When to Read External Files

Situation	File to Read	Purpose
Need algorithm details	references/algorithm.md	Distance calculation, linkage rules, and clustering assumptions
Need to run analysis or inspect CLI entrypoint behavior	scripts/main.R	Execute the workflow and inspect argument parsing, defaults, required flags, and sourced modules
Need workflow implementation details	scripts/run_analysis.R	See orchestration order, temp workspace handling, and output generation
Need logging or warning behavior