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copy-number-correction

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

When to use

• Correcting copy-number artifacts in CRISPR-Cas9 screens
• Diagnosing essentiality at amplified loci
• Choosing between CRISPRcleanR, CERES, and Chronos
• Deciding whether CN correction is needed before MAGeCK or BAGEL2
• Switching from Cas9 to CRISPRi to bypass artifacts
• Applying unsupervised pre-hoc correction
• Applying joint CN and gene-effect modeling

When not to use

• CRISPRi or CRISPRa screens
• Base editing screens
• Prime editing screens

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