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tooluniverse-cancer-genomics-tcga

TCGA/GDC cancer genomics analysis — cohort construction, clinical metadata retrieval, somatic mutation frequencies, survival analysis, and multi-omics integration. Use for TCGA-BRCA-style cohort studies, mutation prevalence by cancer type, survival-by-mutation analysis, and pan-cancer driver discovery. Always cancer-type-specific (don't use pan-cancer counts without cohort context).

76

Quality

95%

Does it follow best practices?

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SecuritybySnyk

Passed

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SKILL.md
Quality
Evals
Security

Quality

Content

90%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 high-quality, action-oriented skill body with executable examples, clear phasing, and strong reasoning guidance for interpretation. The main gap is the absence of explicit validation feedback loops and some API reference content that could be offloaded to a separate file.

Suggestions

Add explicit validation checkpoints where raw tool output should be sanity-checked (e.g., 'confirm case_count > 0 before survival analysis; if pValue missing, gene_symbol split may have failed') to lift workflow_clarity.

Move the per-tool API detail and Tool Quick Reference into a references/ file (e.g., TOOLS.md), keeping SKILL.md as an overview that signals it, to improve progressive_disclosure.

DimensionReasoningScore

Conciseness

Lean and efficient throughout — it assumes Claude's competence (no explanation of what cancer, TCGA, or survival analysis is) and every section earns its place with param lists, return shapes, and tight examples rather than prose padding.

5 / 5

Actionability

Fully executable copy-paste-ready code per phase with real values (e.g., EGFR chr7:55019017-55211628, KRAS G12C), explicit required params, aliases, and concrete return-field access like 'surv["data"]["overallStats"]["pValue"]'.

5 / 5

Workflow Clarity

The 6-phase pipeline is clearly sequenced with caveats (sample size, retrospective-not-treatment-stratified, n<20 unreliability), but the steps are read-only analysis rather than destructive/batch operations, and there are no explicit validate→fix→retry feedback checkpoints, keeping it just below 5.

4 / 5

Progressive Disclosure

Good structure with a Quick Reference table, per-phase sections, and well-signaled sibling-skill references ('See tooluniverse-data-wrangling skill for pagination...'), but the ~330 lines of per-tool API detail are largely inlined rather than split into a separate reference file, leaving minor organization gaps.

4 / 5

Total

18

/

20

Passed

Description

100%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, specific description that answers what and when with comprehensive trigger coverage and clear niche boundaries. Third-person voice is used throughout, and the scope-limiting caveat effectively reduces conflict with adjacent skills.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'cohort construction, clinical metadata retrieval, somatic mutation frequencies, survival analysis, and multi-omics integration' — giving comprehensive coverage of the skill's capabilities.

5 / 5

Completeness

Explicitly answers both 'what' (the five analysis actions) and 'when' via 'Use for TCGA-BRCA-style cohort studies, mutation prevalence by cancer type, survival-by-mutation analysis, and pan-cancer driver discovery' with concrete trigger phrases.

5 / 5

Trigger Term Quality

Natural terms users would say are well covered with synonyms: 'TCGA/GDC', 'cancer cohort', 'somatic mutation', 'Kaplan-Meier', 'survival analysis', 'mutation frequency', 'CNV', and concrete IDs like 'TCGA-BRCA-style'.

5 / 5

Distinctiveness Conflict Risk

Clear TCGA/GDC cancer-genomics niche with explicit boundary guidance ('Always cancer-type-specific... don't use pan-cancer counts without cohort context') and a NOT-for section in the body separating it from precision-oncology and rare-disease skills, giving minimal conflict risk.

5 / 5

Total

20

/

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.

Validation15 / 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
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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