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consensus-clustering-analysis

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.

Quality

87%

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SKILL.md
Quality
Evals
Security

Quality

Content

78%Weight 40%Scale 1-5

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

A well-structured, highly actionable skill body with exemplary progressive disclosure via the external-files routing table. The main deductions are the nonexistent tests/data paths in the smoke check, output verification absent as a workflow checkpoint, and a few low-value sections (Methods restatement, Implementation Checklist, version footer).

Suggestions

Fix the smoke-check paths or ship the test data: the Testing section invokes `tests/data/expression_matrix.csv` and `tests/data/groups.csv`, but no `tests/` directory exists in the bundle (despite the checklist claiming 'Test data provided'), so the command fails as written.

Fold output verification into the workflow: add an explicit Step 5 checkpoint (e.g., inspect `Cluster_res.csv` for the `is_best` row and confirm the plot PDFs exist) instead of leaving validation only in the separate Testing section.

Trim low-yield sections: the Methods restatement of standard ConsensusClusterPlus/PAC behavior, the Implementation Checklist (build meta-commentary), and the 'Last updated | Version' footer add tokens without usage value.

DimensionReasoningScore

Conciseness

The body is lean and table-driven (arguments, input formats, outputs, error codes) with almost no padding, but a few tokens don't earn their place: the Methods section restates standard ConsensusClusterPlus behavior ("Repeated subsampling is used to estimate cluster stability"), the Implementation Checklist is meta-commentary about the build rather than usage guidance, and a "Last updated: 2026-04-17 | Version" footer adds time-sensitive noise. Not anchor 5 because of these trims; well above anchor 3 since there is no real over-explanation of concepts Claude already knows.

4 / 5

Actionability

Commands are fully executable and copy-paste ready: a complete Usage invocation, an argument table with types/defaults, three flag-varying examples, and validation commands. The gap: the smoke check references `tests/data/expression_matrix.csv` and `tests/data/groups.csv`, but no `tests/` directory exists in the bundle, so that command fails as written — a minor gap that keeps it below the fully-executable anchor 5.

4 / 5

Workflow Clarity

Four sequenced steps (Validate Input → Prepare Matrix → Run Clustering → Generate Outputs) with an explicit validation step up front, an error-code table routing recovery, and testing/validation commands for outputs. Anchor 5 is not met because output verification lives only in the Testing section rather than as an explicit checkpoint in the workflow, and the workflow bullets describe rather than instruct (e.g., "Evaluate supported distance and clustering algorithm combinations" without naming the combinations).

4 / 5

Progressive Disclosure

A "When to Read External Files" routing table maps each situation to exactly the right bundle file, and all four referenced paths (`references/algorithm.md`, `scripts/main.R`, `references/troubleshooting.md`, `references/cli-guide.md`) exist one level deep. The body stays an overview while details live in references and scripts — this matches the anchor-5 structure.

5 / 5

Total

17

/

20

Passed

Description

92%Weight 40%Scale 1-5

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 description: third-person voice, concrete capability list tied to a named tool, an explicit 'Use when' trigger clause, and an explicit NOT-for boundary. Only minor synonym coverage (e.g., the literal phrase 'consensus clustering') is missing from the trigger terms.

DimensionReasoningScore

Specificity

The description lists multiple concrete actions — "identifying stable sample subtypes", "PAC-based model selection", and "consensus matrix/CDF visualization" — anchored to a named tool (ConsensusClusterPlus) and input type (bulk expression matrices), giving comprehensive coverage of the skill's capabilities. Anchor 4 would apply if actions were listed with notable gaps, but nothing material to the skill's purpose is missing.

5 / 5

Completeness

Both what and when are explicit: "Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization" states the capability and the concrete trigger condition in one clause, matching the anchor-5 pattern. The when clause could hardly be more specific.

5 / 5

Trigger Term Quality

Natural terms users would say are present: "ConsensusClusterPlus", "bulk expression matrices", "sample subtypes", "consensus matrix", "PAC". A few natural phrasings are missing — the literal phrase "consensus clustering", synonyms like "subtype discovery"/"unsupervised clustering", and input file formats (.csv) — which keeps it just below the comprehensive-synonyms anchor 5 but clearly above anchor 3's partial coverage.

4 / 5

Distinctiveness Conflict Risk

A clear niche (ConsensusClusterPlus subtype discovery on bulk expression data) is reinforced by an explicit exclusion list — "NOT for: differential expression analysis, single-cell clustering workflows, or non-expression tables" — which sharply separates it from the most confusable adjacent skills. Conflict risk is minimal.

5 / 5

Total

19

/

20

Passed

Validation

93%

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

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository

aipoch/medical-research-skills

Path

awesome-med-research-skills/Data Analysis/consensus-clustering-analysis/SKILL.md

Reviewed

Table of Contents

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