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

When to Use

✅ Use this skill when:

• Analyzing genome-wide viability screens to identify essential genes required for cell survival
• Performing drug resistance screens to find genes whose knockout confers resistance
• Conducting drug sensitivity screens to identify synthetic lethal interactions
• Performing quality control assessment of CRISPR screen data before downstream analysis
• Comparing multiple treatment conditions (e.g., drug vs DMSO, hypoxia vs normoxia)
• Validating screen quality before publication or further experimental validation
• Generating hit lists for secondary screens or validation experiments

❌ Do NOT use when:

• Analyzing single-cell CRISPR data (Perturb-seq, CROP-seq) → Use specialized single-cell analysis tools
• Working with arrayed CRISPR screens (well-by-well format) → Use standard differential expression analysis
• Performing CRISPR activation (CRISPRa) or interference (CRISPRi) screens → May need adjusted normalization
• Requiring Bayesian or MAGeCK statistical analysis → This tool uses RRA; use MAGeCK for alternative algorithms
• Analyzing small custom libraries (<1000 sgRNAs) → Statistical power may be insufficient
• Time-course CRISPR screens → Requires specialized trajectory analysis methods

Related Skills:

• 上游 (Upstream): crispr-grna-designer, fastqc-report-interpreter
• 下游 (Downstream): go-kegg-enrichment, pathway-visualization, hit-validation-planner

Integration with Other Skills

Upstream Skills:

• crispr-grna-designer: Design sgRNA libraries before screening; validate library composition
• fastqc-report-interpreter: Assess sequencing quality before CRISPR screen analysis
• alignment-quality-checker: Verify sgRNA alignment rates and mapping quality