tooluniverse-crispr-screen-analysis

Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic lethal interactions, and drug targets. Perform sgRNA count processing, gene-level scoring (MAGeCK, BAGEL), quality control, pathway enrichment, and drug target prioritization. Use for CRISPR screen analysis, gene essentiality studies, synthetic lethality detection, functional genomics, drug target validation, or identifying genetic vulnerabilities.

Quality

90%

Does it follow best practices?

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Securityby

Low

Low-risk findings worth noting

Quality

Content

80%

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A highly actionable and well-sequenced skill with concrete executable code and strong validation feedback loops across an 8-phase workflow. Its main weakness is token efficiency and progressive disclosure: the entire codebase lives inline in SKILL.md with no reference files to offload detailed material.

Suggestions

Split the per-phase full function definitions into reference files (e.g., PHASE1_PROCESSING.md, SCORING.md) and keep SKILL.md as a concise overview with one-level-deep links, improving both conciseness and progressive_disclosure.

Move the long literature-style References section and the Advanced Use Cases into a separate REFERENCE.md or EXAMPLES.md so the top-level skill stays lean.

Tighten prose that restates domain basics Claude already knows (e.g., 'CRISPR screens enable genome-wide functional genomics by systematically perturbing genes...') to earn back tokens in the overview.

Dimension	Reasoning	Score
Conciseness	The body is ~900 lines of dense executable code plus commentary, far exceeding what an overview needs; while mostly accurate, the monolithic inline codebook (full function definitions for every phase) is heavy for a SKILL.md and could be split into reference files to respect token budget.	2 / 3
Actionability	Provides complete, executable Python functions with realistic data formats (sgRNA count matrices, design tables) and concrete ToolUniverse tool calls (Enrichr, DGIdb, PubMed), copy-paste ready per the rubric.	3 / 3
Workflow Clarity	An explicit 8-phase sequence with QC/validation checkpoints (column validation, low-count filtering, reference-set adequacy checks, error-recovery troubleshooting) gives clear feedback loops for the destructive/batch operations involved.	3 / 3
Progressive Disclosure	No bundle files exist and the entire workflow is inline as one monolithic SKILL.md; references to literature are present but there is no one-level-deep split into reference files for the extensive API/method detail, which the rubric rewards at 3.	2 / 3
	Total	10 / 12 Passed

Description

100%

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 enumerates concrete capabilities and provides explicit 'Use when...' trigger guidance with natural user vocabulary. It is third-person, concise, and well-scoped to a distinct niche.

Dimension	Reasoning	Score
Specificity	Lists many concrete actions — 'sgRNA count processing', 'gene-level scoring (MAGeCK, BAGEL)', 'quality control', 'pathway enrichment', and 'drug target prioritization' — matching the 'multiple specific concrete actions' anchor.	3 / 3
Completeness	Explicitly states what ('Comprehensive CRISPR screen analysis... Perform sgRNA count processing...') and when ('Use for CRISPR screen analysis, gene essentiality studies...'), satisfying the 'both what AND when with explicit triggers' anchor.	3 / 3
Trigger Term Quality	Covers natural user phrasing broadly — 'CRISPR screen analysis', 'gene essentiality studies', 'synthetic lethality detection', 'functional genomics', 'drug target validation', 'identifying genetic vulnerabilities' — good coverage of terms users would actually say.	3 / 3
Distinctiveness Conflict Risk	Niche is clearly delimited to CRISPR screen analysis with distinct triggers (MAGeCK, BAGEL, sgRNA, DepMap), unlikely to fire for unrelated skills.	3 / 3
	Total	12 / 12 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
skill_md_line_count	SKILL.md is long (901 lines); consider splitting into references/ and linking	Warning

	Total	15 / 16 Passed

Repository: wu-yc/LabClaw
Path: skills/bio/tooluniverse-crispr-screen-analysis/SKILL.md
Commit: df37802

Reviewed: 2 days ago

Table of Contents

Discovery Implementation Validation

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