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tooluniverse-immune-repertoire-analysis

TCR/BCR repertoire analysis — V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity matching to IEDB, public-clone identification. Use for adaptive immune response characterization, post-treatment immune monitoring, antigen-specific clone tracking, and clonal-expansion analysis in immunotherapy or vaccination studies.

68

Quality

81%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

62%

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

A well-structured, domain-rich skill with a clear 8-phase workflow and concrete ToolUniverse tool integration, but it re-explains known concepts, uses pseudocode helper functions in its Quick Start, and references bundle files that are not actually present.

Suggestions

Remove or compress explanations of well-known concepts (Shannon entropy, Gini coefficient, convergent recombination) and keep only the domain-specific thresholds and operational guidance.

Replace the undefined Quick Start helper functions (load_airr_data, define_clonotypes, etc.) with executable code, or explicitly justify them as pseudocode with a pointer to a real implementation.

Create the referenced ANALYSIS_DETAILS.md and USE_CASES.md files (or remove the See Also pointers) so the progressive-disclosure references resolve to real bundle files.

DimensionReasoningScore

Conciseness

Mostly efficient domain content, but it re-explains concepts Claude already knows (e.g. 'Shannon entropy: Overall diversity (higher = more diverse)', definitions of convergent recombination and Gini coefficient) and the Domain Reasoning / Interpretation Guidance sections could be tightened; not score 3 because not every token earns its place, and not score 1 because the bulk is actionable domain knowledge rather than generic filler.

2 / 3

Actionability

Concrete tool calls with real parameters (e.g. 'BVBRC_search_epitopes' with taxon_id="2697049", 'sequence_contains' for motif search) are strong, but the Quick Start relies on undefined helper functions (load_airr_data, define_clonotypes, calculate_diversity, detect_expanded_clones, query_epitope_database) that are effectively pseudocode and not copy-paste executable; not score 3 because the code is not fully executable, and not score 1 because there is genuine concrete guidance beyond vague direction.

2 / 3

Workflow Clarity

An 8-phase workflow is clearly sequenced with verification guidance (rarefaction plateau checks, an evidence-grading table, and synthesis questions); this is a read-only analysis workflow so the destructive/batch validation cap does not apply, and not score 2 because checkpoints are explicit rather than merely implicit.

3 / 3

Progressive Disclosure

The 'See Also' section signals one-level-deep references (ANALYSIS_DETAILS.md, USE_CASES.md), but those files do not exist in the bundle and substantial detail is inlined in SKILL.md that could be split out; not score 3 because the referenced files are missing and the split is incomplete, and not score 1 because references are clearly signaled rather than deeply nested.

2 / 3

Total

9

/

12

Passed

Description

100%

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, third-person description that names concrete capabilities and gives an explicit 'Use for' trigger clause covering multiple immunology contexts. It is comprehensive, distinctive, and free of vague fluff.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity matching to IEDB, public-clone identification' — matching the anchor for multiple specific concrete actions, and is comprehensive rather than partial, so it is not the level below.

3 / 3

Completeness

Clearly answers both what (the analysis capabilities) and when via an explicit 'Use for adaptive immune response characterization, post-treatment immune monitoring...' clause; it is not the level below because the when is explicit, not merely implied.

3 / 3

Trigger Term Quality

Natural domain terms a practitioner would actually say — 'TCR/BCR repertoire analysis', 'clonality scoring', 'clonal-expansion analysis', 'immune monitoring', 'immunotherapy or vaccination studies' — give good coverage; not the level below because common variations are present rather than just one keyword.

3 / 3

Distinctiveness Conflict Risk

A clear niche (TCR/BCR immune repertoire analysis) with distinct triggers unlikely to fire for unrelated skills; not the level below because the domain and triggers are specific, not generic.

3 / 3

Total

12

/

12

Passed

Validation

100%

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

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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