tooluniverse-gene-regulatory-networks

Gene regulatory network analysis — TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, perturbation evidence (knockout/overexpression). Use for 'which TF regulates gene X', 'which genes does TF Y target', regulatory pathway reconstruction. Distinguishes direct (binding) vs indirect (co-expression) regulatory evidence.

Quality

87%

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Securityby

Low

Low-risk findings worth noting

Quality

Content

82%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.

The body is a well-structured, highly actionable tool catalog with a clear phased workflow and useful guardrail sections. It is concise for its scope and well-organized, though it could benefit from explicit validation/feedback checkpoints in its analytical workflow.

Suggestions

Add explicit validation/feedback checkpoints in the workflow (e.g., 'if a JASPAR search returns no matrices, retry with a synonym or broader collection') to strengthen error recovery.

Consider extracting the per-tool parameter reference tables into a references/ file, keeping SKILL.md as a leaner overview that points to the full tool catalog.

Trim the opening paragraph's conceptual framing ('A TF binding near a gene doesn't prove regulation...') into a tighter one-liner, since Claude already understands evidence hierarchy.

Dimension	Reasoning	Score
Conciseness	Mostly efficient for a ~15-tool catalog — it assumes Claude's domain competence and avoids generic padding, with only minor instances of explanation that could be trimmed.	4 / 5
Actionability	Fully actionable: concrete tool names, parameter tables, copy-paste JSON examples, and return schemas covering the common cases for every phase.	5 / 5
Workflow Clarity	A clear phased sequence (Phase 0 input disambiguation through Phase 7 enrichment) with guardrails via 'LOOK UP DON'T GUESS' and Common Mistakes; lacks explicit validate→retry feedback loops, though the skill is analytical rather than destructive.	4 / 5
Progressive Disclosure	Well-organized single-file structure with clear headers (When to Use, Workflow, Common Mistakes, Common Use Patterns, Evidence Grading) and easy navigation; no bundle files are needed for this self-contained tool catalog.	4 / 5
	Total	17 / 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, specific description that clearly states capabilities and provides natural trigger phrases for when to use the skill. It distinguishes direct vs indirect regulatory evidence, reinforcing its distinct niche. Trigger-term synonym coverage could be slightly broader but is otherwise excellent.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, perturbation evidence' — with comprehensive coverage of the domain.	5 / 5
Completeness	Explicitly answers both what (TF-target inference, motif scanning, eQTL integration, perturbation evidence) and when ('Use for ...') with concrete trigger phrases.	5 / 5
Trigger Term Quality	Includes natural user phrases ('which TF regulates gene X', 'which genes does TF Y target', 'regulatory pathway reconstruction'), though synonym/variation coverage is good rather than exhaustive.	4 / 5
Distinctiveness Conflict Risk	Clear niche in gene regulatory network analysis with distinct, domain-specific triggers and minimal overlap with other skills.	5 / 5
	Total	19 / 20 Passed

Validation

100%

Warnings & errors only

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

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: mims-harvard/ToolUniverse
Path: plugin/skills/tooluniverse-gene-regulatory-networks/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

Table of Contents

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