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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%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

63%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, domain-rich skill body with a clear 8-phase workflow and a thoughtful evidence-grading/synthesis framework. Its main weaknesses are pseudocode in the Quick Start (undefined helper functions) and dangling references to bundle files that do not exist.

Suggestions

Make the Quick Start executable: either implement the helper functions (load_airr_data, define_clonotypes, calculate_diversity, detect_expanded_clones, query_epitope_database) in a bundled script, or rewrite the example using the real ToolUniverse API calls already named in Phase 7.

Create the referenced ANALYSIS_DETAILS.md and USE_CASES.md (or remove the "See Also" links) so navigation targets are real; move the per-phase detail and reasoning framework into ANALYSIS_DETAILS.md to slim SKILL.md into a true overview.

Add explicit verification checkpoints inside the phases (e.g., "confirm rarefaction plateau before trusting richness estimates") to match the validation bar the evidence-grading section implies.

DimensionReasoningScore

Conciseness

Dense and largely assumes Claude's competence, supplying domain-specific values Claude would not know (Gini > 0.3, clonality > 0.2, Shannon 5–12); the only slack is the Overview re-listing the same 8 phases that are each expanded immediately below.

4 / 5

Actionability

The Quick Start calls undefined helper functions (load_airr_data, define_clonotypes, calculate_diversity, detect_expanded_clones, query_epitope_database) — pseudocode, not executable; real tool names and concrete parameters (taxon_id="2697049", sequence_contains) partially compensate but key execution detail is missing.

3 / 5

Workflow Clarity

Eight clearly sequenced phases plus an evidence-grading table and synthesis questions that act as an interpretation checkpoint; this is read-only analysis so the destructive/batch validation cap does not apply, but there are no explicit validate-then-continue checkpoints within the phases.

4 / 5

Progressive Disclosure

Sections are organized, but detailed phase content and the reasoning framework are inlined rather than split out, and the "See Also" references to ANALYSIS_DETAILS.md and USE_CASES.md point to files that are NOT present in the bundle (references/, scripts/, assets/ are empty) — dangling, weakly-signaled references.

3 / 5

Total

14

/

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, well-constructed description: concrete capabilities, explicit use-when trigger guidance, comprehensive domain keywords, and a distinct niche with low conflict risk. It assumes the target user's vocabulary without padding.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — "V(D)J segment usage", "CDR3 sequence diversity", "clonality scoring", "antigen specificity matching to IEDB", "public-clone identification" — giving comprehensive coverage of the skill's capabilities.

5 / 5

Completeness

Explicitly answers both what (the five analysis actions) and when ("Use for adaptive immune response characterization, post-treatment immune monitoring, antigen-specific clone tracking, and clonal-expansion analysis in immunotherapy or vaccination studies") with concrete trigger phrases.

5 / 5

Trigger Term Quality

Comprehensive natural domain terms a user would say — "TCR/BCR repertoire analysis", "clonality", "CDR3", "V(D)J", "clonal-expansion", "immunotherapy", "vaccination" — including synonyms (TCR/BCR, clonality/clonal-expansion).

5 / 5

Distinctiveness Conflict Risk

TCR/BCR repertoire analysis is a clear specialist niche with distinct triggers; minimal overlap risk with other skills. No first/second-person voice, so no specificity penalty applies.

5 / 5

Total

20

/

20

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

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