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crispr-screen-analyzer

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Process CRISPR screening data to identify essential genes and hit candidates. Performs quality control, statistical analysis (RRA), and hit calling for pooled CRISPR screens including viability screens and drug resistance/sensitivity studies.

scientific-skills/Data Analysis/crispr-screen-analyzer/SKILL.md

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

# CRISPR Screen Analyzer

Analyze pooled CRISPR screening data to identify essential genes, drug resistance/sensitivity candidates, and screen quality metrics. Supports Robust Rank Aggregation (RRA) analysis, quality control assessment, and hit identification for functional genomics studies.

**Key Capabilities:**
- **Quality Control Assessment**: Calculate Gini index, read depth, and dropout metrics to evaluate screen quality
- **Log Fold Change Calculation**: Compute sgRNA-level fold changes between treatment and control conditions
- **Statistical Analysis**: Perform Robust Rank Aggregation (RRA) to identify significantly enriched or depleted sgRNAs
- **Hit Identification**: Apply FDR and fold change thresholds to identify candidate genes
- **Multi-Sample Support**: Process multiple replicates and treatment conditions simultaneously

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