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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.

65

Quality

77%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

Fix and improve this skill with Tessl

tessl review fix ./plugins/tooluniverse/skills/tooluniverse-spatial-omics-analysis/SKILL.md

The canonical home for this skill is tooluniverse-spatial-omics-analysis in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

62%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.

Well-structured content with a clear multi-phase workflow and good progressive-disclosure signaling, but it lacks executable code despite instructing computation and the referenced reference files are missing from the bundle. Actionability and progressive disclosure are the weakest dimensions.

Suggestions

Add at least one executable Python snippet per analysis phase to satisfy the 'COMPUTE, DON'T DESCRIVE' principle and raise actionability.

Include the referenced files (phase-procedures.md, tool-reference.md, reference-data.md, report-template.md) in the bundle, or remove the references if the content is meant to be self-contained.

Make per-phase validation checkpoints explicit (e.g., 'after Phase 2, confirm FDR<0.05 before proceeding') to strengthen workflow clarity.

DimensionReasoningScore

Conciseness

The body is dense and mostly efficient, assuming domain competence without explaining basics, but the closing Summary section recapitulates earlier content and a few tables could be trimmed.

4 / 5

Actionability

Concrete guidance is present via specific tool names and parameter tables, but despite a 'COMPUTE, DON'T DESCRIBE' directive there are no executable code examples — only reference-style tables and phase descriptions.

3 / 5

Workflow Clarity

A clear 8-phase sequence (Phase 0–8) with a report-first principle and completeness checklist is present, but per-phase validation checkpoints are implied rather than made explicit.

4 / 5

Progressive Disclosure

References are clearly signaled one-level-deep ('See phase-procedures.md', 'See report-template.md'), but the referenced bundle files are absent from the package, so the disclosure structure is only partially realized.

3 / 5

Total

14

/

20

Passed

Description

92%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 with explicit what-and-when structure and excellent trigger-term coverage for spatial omics platforms. The only weakness is that the listed actions lean on abstract noun phrases rather than sharp verbs, slightly reducing specificity.

DimensionReasoningScore

Specificity

Lists several concrete actions ('domain-by-domain characterization, cell-type composition, spatial gene expression patterns, RNA+protein+metabolite integration') but they are phrased as abstract noun phrases rather than crisp verbs, leaving minor gaps in coverage clarity.

4 / 5

Completeness

Explicitly answers both 'what' (transforms SVGs, domain annotations, and tissue context into biological insights) and 'when' via an explicit 'Use for' clause with concrete trigger platforms.

5 / 5

Trigger Term Quality

Comprehensive coverage of natural platform terms users say ('Visium, MERFISH, seqFISH, Slide-seq, spatial proteomics, and spatial multi-omics interpretation') with strong synonym/extension coverage.

5 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (spatial multi-omics interpretation) with platform-specific triggers, giving it minimal conflict risk with other skills.

5 / 5

Total

19

/

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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