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tooluniverse-spatial-omics-analysis

Spatial multi-omics interpretation pipeline. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into biological insights via domain-by-domain characterization, cell-type composition, spatial gene expression patterns, RNA+protein+metabolite integration. Use for Visium, MERFISH, seqFISH, Slide-seq, spatial proteomics, and spatial multi-omics interpretation. Goes beyond statistics to disease mechanisms and therapeutic opportunities.

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 dense, well-structured pipeline skill with concrete tooling and clear phase sequencing, weakened by redundancy between its summary and body and by references to bundle files that are not present.

Suggestions

Provide the missing bundle files (phase-procedures.md, tool-reference.md, reference-data.md, report-template.md, test_spatial_omics.py) referenced in the body, or remove the references so navigation is not broken.

Add at least one concrete example — a sample tool call and a Python snippet — to satisfy the 'COMPUTE, DON'T DESCRIBE' principle and lift actionability.

Trim the redundant 'Summary' section and consolidate 'KEY PRINCIPLES' with the standalone directive sections to reduce token cost.

DimensionReasoningScore

Conciseness

Mostly efficient with concrete phase/tool listings, but the terminal 'Summary' section restates the phases and the 'KEY PRINCIPLES' list overlaps with standalone sections like 'LOOK UP, DON'T GUESS' and 'COMPUTE, DON'T DESCRIBE'.

3 / 5

Actionability

Concrete tool function names and a parameter table make the guidance largely executable, but no example tool calls or Python snippets are provided despite the skill's own 'COMPUTE, DON'T DESCRIBE' directive.

4 / 5

Workflow Clarity

Phases 0–8 are clearly sequenced with 'ALWAYS FIRST' ordering, a report-first progressive-population loop, and a terminal completeness checklist, though inter-phase validation checkpoints are only implicit.

4 / 5

Progressive Disclosure

References are clearly signaled and one level deep (phase-procedures.md, report-template.md, tool-reference.md, reference-data.md), but none of these bundle files actually exist in the skill directory, so the promised navigation is broken.

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 well-crafted description that concretely states capabilities, gives explicit use-when trigger phrases with natural platform keywords, and carves out a distinct niche. Third-person voice is used correctly throughout.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'domain-by-domain characterization, cell-type composition, spatial gene expression patterns, RNA+protein+metabolite integration' — giving comprehensive coverage of the pipeline's capabilities.

5 / 5

Completeness

Explicitly answers both what ('Transforms spatially variable genes ... into biological insights via ...') and when ('Use for Visium, MERFISH ...') with concrete trigger phrases.

5 / 5

Trigger Term Quality

Comprehensive natural trigger terms a researcher would actually say: 'Visium, MERFISH, seqFISH, Slide-seq, spatial proteomics, and spatial multi-omics interpretation' cover the relevant platforms and synonyms.

5 / 5

Distinctiveness Conflict Risk

Clear niche (spatial multi-omics interpretation) with distinct platform-named triggers that minimize overlap with adjacent bioinformatics skills.

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

Table of Contents

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