domains / families / science / crispr-screen-pipeline

crispr-screen-pipeline

separate

End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, matching the hit-calling method to the experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.

When to use

• analyzing pooled CRISPR screens end-to-end
• analyzing single-cell CRISPR screens
• matching hit-calling method to experimental design
• integrating copy-number correction into the pipeline
• branching workflow for single-cell variants
• branching workflow for combinatorial screens
• branching workflow for base-editor screens
• branching workflow for prime-editor screens

When not to use

• internals of any one step

Skill page

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