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umap-tsne-analysis

Use when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE coordinates and plots for group separation assessment. NOT for: differential expression testing, single-cell workflows requiring dedicated embeddings pipelines, or analyses without a sample grouping file.

66

Quality

83%

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SKILL.md
Quality
Evals
Security

Quality

Content

73%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.

The body is a well-structured, highly actionable operational document with clear sequencing, validation, and error recovery. Its weaknesses are moderate padding (textbook method explanations, an implementation checklist, a duplicated dependency table) and references to bundle files that do not actually exist.

Suggestions

Remove the 'Methods' concept explanations (t-SNE/UMAP/normalization definitions Claude already knows) and the 'Implementation Checklist' section, or move both to a reference file — this would recover the conciseness lost to padding.

Delete the inline 'Dependency Baseline' table (it duplicates dependencies.lock.tsv) or actually ship dependencies.lock.tsv and reference it in one line.

Fix dangling bundle references: either include the tests/ directory (test_skill.R, run_smoke_test.R, data/) that the Testing section depends on, or remove those commands; similarly resolve the tests/output validation commands against the shipped bundle.

DimensionReasoningScore

Conciseness

The body mostly uses tight, efficient tables, but it pads several sections: the 'Methods' section re-teaches what t-SNE and UMAP are ('t-SNE is a non-linear dimensionality reduction method that preserves local neighborhood structure'), the 13-item 'Implementation Checklist' is development meta-noise irrelevant to running the skill, and the 'Dependency Baseline' table duplicates dependencies.lock.tsv. This fits 'mostly efficient but includes some unnecessary explanation' rather than the 2 anchor, since the padding is a minority of the document.

3 / 5

Actionability

The main path is fully executable: copy-paste install and usage commands, a complete arguments table, concrete input/output specs, and an error-code-to-solution table. However, the Testing section's commands reference tests/data/, tests/test_skill.R, and tests/run_smoke_test.R, and the Dependency Baseline section references dependencies.lock.tsv — none of which exist in the bundle — so those commands are not runnable as shipped, a minor gap consistent with the 4 anchor.

4 / 5

Workflow Clarity

The 4-step workflow is clearly sequenced with an explicit validation step up front (Step 1: validate groups, samples, column alignment), error-to-solution feedback loops with re-run guidance ('Install dependencies first, then re-run to expose any file-related errors'), and post-run verification commands (ls of output dirs, wc -l on coordinate CSVs). This matches the 5 anchor: clear sequence with explicit validation and recovery loops.

5 / 5

Progressive Disclosure

The 'When to Read External Files' table clearly signals one-level-deep references (references/algorithm.md, troubleshooting.md, cli-guide.md — all real files) by situation, which is excellent. Minor gaps keep it below 5: the body also points to nonexistent paths (tests/, dependencies.lock.tsv), and the full inline Arguments table duplicates content that belongs in the cli-guide reference.

4 / 5

Total

16

/

20

Passed

Description

87%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: concrete capabilities, natural trigger terms, explicit what/when clauses, and an explicit negative boundary. It is specific, well-scoped, and unlikely to fire for the wrong task.

DimensionReasoningScore

Specificity

The description lists several concrete actions — 'performing sample-level dimensionality reduction and visualization', 'generating UMAP and/or t-SNE coordinates and plots for group separation assessment' — with minor coverage gaps (e.g., no mention of normalization or output formats). It is below the 5 anchor's comprehensive multi-action coverage but above the 3 anchor's 1-2 actions.

4 / 5

Completeness

It explicitly answers both 'what' ('generating UMAP and/or t-SNE coordinates and plots for group separation assessment') and 'when' ('Use when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file'), with concrete trigger phrases matching the 5 anchor's pattern.

5 / 5

Trigger Term Quality

It includes the natural terms users would say for this need: 'UMAP', 't-SNE', 'abundance or OTU-style matrices', 'group file', 'dimensionality reduction', 'visualization'. A few natural synonyms are missing (e.g., 'ordination', 'microbiome', file extensions like .csv), so it fits the 4 anchor rather than the comprehensive 5 anchor.

4 / 5

Distinctiveness Conflict Risk

The skill occupies a clear niche (sample-level UMAP/t-SNE on abundance matrices with a companion group file) and the explicit 'NOT for:' exclusion list (differential expression testing, single-cell workflows, analyses without a grouping file) actively minimizes conflict with related skills, matching the 5 anchor.

5 / 5

Total

18

/

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
Reviewed

Table of Contents

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