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mageck

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Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces gene hit rankings with effect sizes and FDR. Use for new knockout, CRISPRi, or CRISPRa screen analysis, enrichment or depletion contrasts, and MAGeCK count/test workflows; existing public dependency-score lookup belongs to DepMap.

When to use

• Use this skill to count existing sequencing reads against a supplied guide library or compare already-counted pooled screens. Deliver the count matrix, QC, guide and gene results, contrast provenance, and a short interpretation of enrichme…

When not to use

• guide design
• inferring gene function from a hit alone
• existing public dependency-score lookup

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