hierarchical-clustering-plot

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.

Quality

80%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

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Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

Highly actionable, well-structured content with excellent progressive disclosure and a clear sequenced workflow; the main drag is conciseness, where build-meta and reference-grade material is inlined rather than deferred to the referenced files.

Suggestions

Remove or relocate the 'Implementation Checklist' — it describes how the skill was built rather than guidance for executing it, and adds ~19 lines of token cost with no execution value.

Move the 15-row 'Common Errors' table body into references/troubleshooting.md (already referenced) and keep only a one-line pointer plus the most frequent errors inline.

Drop the duplicated 'Trigger keywords' / 'Not for' bullet list under 'When to Use' since the same information is already in the frontmatter description.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with concrete tables and commands, but padded by an internal-facing 'Implementation Checklist' of 19 build-meta items, a duplicated trigger-keyword list, and a 15-row error table whose bulk could live in the referenced troubleshooting file; fits 'mostly efficient but could be tightened' rather than the lean level-4 anchor.	3 / 5
Actionability	Provides fully executable, copy-paste-ready Rscript invocations with all flags, concrete CSV input snippets, an arguments table with defaults, and multiple worked examples covering the common cases.	5 / 5
Workflow Clarity	A clearly sequenced four-step workflow (validate → align → cluster → save) with an explicit validation step and an error-handling table for recovery, but the validation commands are pointed to via 'READ' pointers rather than given as an inline validate-fix-retry loop, leaving minor checkpoint gaps.	4 / 5
Progressive Disclosure	A 'When to Read External Files' table maps situations to specific one-level-deep reference and script files, all of which exist in the bundle (references/, scripts/, tests/), giving clear overview navigation with appropriately split content.	5 / 5
	Total	17 / 20 Passed

Description

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Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong, well-scoped description with explicit trigger guidance and clear boundary exclusions; its only weakness is that it names a single concrete action rather than a comprehensive set of capabilities.

Dimension	Reasoning	Score
Specificity	Names the domain and inputs concretely ('sample-level hierarchical clustering dendrogram from a bulk expression matrix and sample annotation table') but describes essentially one action — building the dendrogram — rather than a comprehensive set of specific actions, fitting the '1-2 concrete actions' anchor rather than the 'several specific actions' level 4.	3 / 5
Completeness	Clearly answers both 'what' (build a sample-level dendrogram from an expression matrix and annotation table) and 'when' ('Use when... especially for QC, batch inspection, or sample similarity assessment') with concrete trigger phrases, matching the top anchor.	5 / 5
Trigger Term Quality	Explicit 'Trigger keywords: hierarchical clustering, dendrogram, sample QC, batch inspection, sample similarity' gives good natural-term coverage a user would actually say, but lacks synonyms or file-extension variants that would push it to a 5.	4 / 5
Distinctiveness Conflict Risk	A narrow niche (sample-level bulk-expression dendrograms) plus an explicit 'NOT for: differential expression testing, gene clustering heatmaps, single-cell clustering workflows' exclusion gives clear distinct triggers with minimal conflict risk.	5 / 5
	Total	17 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: aipoch/medical-research-skills
Path: awesome-med-research-skills/Data Analysis/hierarchical-clustering-plot/SKILL.md
Commit: f5ef65b

Reviewed: ~11 hours ago

Table of Contents

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