cerna-analysis

Use when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports and PDF visualization in a single output directory. NOT for: differential expression, single-cell analysis, enrichment analysis, or workflows without a key gene list.

Quality

87%

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Securityby

Passed

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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.

A well-structured, highly actionable skill body with strong progressive disclosure and a clear validated workflow. The main weaknesses are minor redundancy (repeated dependency notes) and a broken tests/data reference in the bundle.

Suggestions

Consolidate the igraph dependency note to a single location (e.g. the Usage block) and remove the duplicates in the 'When to Read External Files' table and Error Handling row to tighten conciseness.

Either add the missing tests/data/gene.txt sample file to the bundle or remove the tests/data references from the 'When to Read External Files' table and Testing examples so referenced paths resolve.

Flesh out the Workflow steps with the inline validation commands and an explicit validate→fix→retry loop rather than terse bullets, to lift workflow clarity to a 5.

Dimension	Reasoning	Score
Conciseness	Mostly efficient and free of basic-concept padding, but the igraph dependency note is repeated in three places and the 'When to Use' section echoes the frontmatter description, leaving minor instances that could be trimmed.	4 / 5
Actionability	Fully executable, copy-paste ready Rscript commands in Usage and Examples, a complete Arguments table with types/defaults, concrete input-format samples, and a cause→solution error table covering common cases.	5 / 5
Workflow Clarity	Clear four-step sequence with explicit validation in Step 1 (validate input) and a Step 3 stop-condition (SKILL_INVALID_DATA) plus an error-handling feedback loop, but the workflow steps are terse bullets without inline validation commands.	4 / 5
Progressive Disclosure	Excellent 'When to Read External Files' table gives well-signaled one-level-deep references (algorithm.md, main.R, troubleshooting.md, cli-guide.md), but the referenced tests/data/ and tests/data/gene.txt paths are absent from the actual bundle.	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 with an explicit 'Use when' trigger, concrete actions, and clear negative-boundary guidance that sharply reduces activation conflicts. The only gap is a lack of synonyms and file extensions in its trigger terms.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'building a ceRNA regulatory network', 'combining bundled miRNA-mRNA and miRNA-lncRNA database files', 'flat-file CSV exports and PDF visualization in a single output directory' — with comprehensive coverage of the task scope.	5 / 5
Completeness	Explicitly answers both what (build network by combining bundled DB files, CSV exports, PDF visualization) and when ('Use when building a ceRNA regulatory network from a key gene list'), with concrete trigger phrases plus NOT-for exclusions.	5 / 5
Trigger Term Quality	Good keyword coverage with natural domain terms ('ceRNA regulatory network', 'key gene list', 'differential expression', 'single-cell analysis'), but no synonyms (e.g. 'competing endogenous RNA') or file extensions, keeping it just below comprehensive.	4 / 5
Distinctiveness Conflict Risk	Clear niche (ceRNA network from a key gene list) reinforced by explicit exclusions ('NOT for: differential expression, single-cell analysis, enrichment analysis'), minimizing conflict risk with adjacent bioinformatics skills.	5 / 5
	Total	19 / 20 Passed

Validation

93%

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 — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: awesome-med-research-skills/Data Analysis/cerna-analysis/SKILL.md
Commit: f5ef65b

Reviewed: ~9 hours ago

Table of Contents

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