gene-protein-expression-matrix-normalization

Use when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory analysis. NOT for count-model normalization such as TPM/DESeq2 size factors, batch correction, or single-cell preprocessing.

Quality

89%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

90%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.

Excellent token efficiency and actionability with a clean one-level-deep reference structure verified against the actual bundle. Workflow clarity is strong but capped slightly below 5 because destructive output overwriting has no explicit pre-write validation checkpoint or feedback loop in the body.

Suggestions

Add an explicit validation checkpoint before overwriting an existing --output_dir (e.g., a confirm step or a --force flag) to close the destructive-operation feedback gap noted in workflow_clarity.

Include a short validate->fix->retry loop for the common SKILL_INVALID_PARAMETER (non-finite value) case so users see the recovery path inline rather than only in troubleshooting.md.

The body references DESCRIPTION for dependencies, but no DESCRIPTION file ships in the bundle; either add it or point dependency info to cli-guide.md.

Dimension	Reasoning	Score
Conciseness	The body is lean and assumes Claude's competence, presenting only executable commands, argument tables, and method formulas without restating what normalization or matrices are; every section earns its place.	5 / 5
Actionability	Fully executable copy-paste-ready CLI commands, a complete argument table, concrete CSV input examples, and per-method formulas cover all common cases and map directly to the bundled scripts.	5 / 5
Workflow Clarity	A clear single-step execution sequence with an explicit error-handling table and troubleshooting reference, but the destructive overwriting of output files lacks a validation checkpoint before overwrite and no validate-fix-retry loop is shown in the body.	4 / 5
Progressive Disclosure	A concise overview with a well-signaled 'When to Read External Files' table pointing one level deep to real bundle files (main.R, algorithm.md, troubleshooting.md, cli-guide.md), all of which exist, with content appropriately split out of the body.	5 / 5
	Total	19 / 20 Passed

Description

88%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-scoped description that clearly states both capability and trigger conditions while proactively excluding adjacent use cases to reduce conflict risk. Minor room to add user-natural synonyms or file extensions for trigger terms.

Dimension	Reasoning	Score
Specificity	Names three concrete normalization actions ('log2 transform, z-score standardization, or min-max scaling') and the target object ('bulk gene or protein expression matrices'), giving comprehensive coverage of the skill's capabilities.	5 / 5
Completeness	Explicitly answers both 'what' (normalize bulk gene/protein expression matrices with log2/z-score/min-max) and 'when' ('Use when normalizing... before downstream visualization or exploratory analysis') with concrete trigger phrasing.	5 / 5
Trigger Term Quality	Strong natural keywords ('normalize', 'log2', 'z-score', 'min-max scaling', 'expression matrices') but lacks common user phrasings or file extensions such as 'scale my matrix', 'CSV', or 'TPM' that a user might say.	4 / 5
Distinctiveness Conflict Risk	The explicit 'NOT for...' exclusion clause (TPM/DESeq2 size factors, batch correction, single-cell preprocessing) carves a clear niche and minimizes conflict with related normalization 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/gene-protein-expression-matrix-normalization/SKILL.md
Commit: f5ef65b

Reviewed: ~11 hours ago

Table of Contents

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