bio-workflows-crispr-screen-pipeline

name	bio-workflows-crispr-screen-pipeline
description	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, choosing the correct hit-calling method by 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.
tool_type	mixed
primary_tool	MAGeCK
workflow	true
depends_on	["crispr-screens/library-design","crispr-screens/screen-qc","crispr-screens/mageck-analysis","crispr-screens/bagel-essentiality","crispr-screens/drugz-chemogenomic","crispr-screens/jacks-analysis","crispr-screens/hit-calling","crispr-screens/copy-number-correction","crispr-screens/batch-correction","crispr-screens/crispresso-editing","crispr-screens/base-editing-analysis","crispr-screens/prime-editing-screens","crispr-screens/perturb-seq-analysis","crispr-screens/combinatorial-screens","crispr-screens/in-vivo-screens"]
qc_checkpoints	[{"after_counting":">65% mapping rate; <0.5% zero-count in plasmid; Gini <0.1 on plasmid"},{"after_qc":"Replicate Pearson on log-counts >0.85; Spearman >0.7; CEGv2 PR-AUC >0.7"},{"after_cn_correction":"Spearman ρ between CN and gene LFC abs <0.05 post-correction"},{"after_hit_calling":"Tier-1 hits = 3-method consensus; Tier-2 = 2 of 3; Tier-3 = single-method exploratory"}]

Version Compatibility

Reference examples tested with: MAGeCK 0.5.9+, BAGEL2 1.0.5+, drugZ Aug 2019+, JACKS 0.2.0+, Chronos 2.0+, CRISPRcleanR 3.0+ (R), Pertpy 0.6+, PRIDICT2, CRISPResso2 2.2.14+, MAGeCKFlute 2.0+, pandas 2.2+, numpy 1.26+, matplotlib 3.8+.

Before using code patterns, verify installed versions match. If versions differ:

• CLI: mageck --version, BAGEL.py fc --help, drugz -h, CRISPResso --version
• Python: pip show pertpy mageck-vispr jacks chronos-cn
• R: packageVersion('CRISPRcleanR'), packageVersion('MAGeCKFlute')

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

CRISPR Screen Pipeline

"Analyze my pooled or single-cell CRISPR screen end-to-end" -> Pick the screen design branch, run guide counting, audit six QC stages, apply copy-number and batch correction as needed, run the design-matched hit-calling method, and consolidate across methods for high-confidence hits.

Pipeline Branches by Screen Design

                    Library Design ([[library-design]])
                              |
                              v
                FASTQ Files -> mageck count -> count matrix
                              |
                              v
                Six-Stage QC ([[screen-qc]])
                              |
        +---------------------+---------------------+
        |                                            |
        v                                            v
  Cancer cell line?                          Non-cancer?
  Apply CN correction                        No CN correction needed
  ([[copy-number-correction]])
        |                                            |
        +---------------------+---------------------+
                              v
                  Multi-batch? Apply batch covariate
                  ([[batch-correction]])
                              |
                              v
                 Pick hit-calling method by design ([[hit-calling]])
                              |
        +-----------+---------+---------+-----------+-----------+
        |           |         |         |           |           |
        v           v         v         v           v           v
    2-cond       Time      Drug      Essential   Multi-       Specialized
    MAGeCK RRA   MAGeCK    drugZ     BAGEL2      screen       (PE/BE/SC/
                 MLE                              JACKS or     in vivo/
                                                  Chronos      combinat)
        |           |         |         |           |           |
        +-----------+---------+---------+-----------+-----------+
                              v
                   Tier-based consensus
                              v
                Orthogonal validation