Genome-Wide CRISPR Knockout Screen Analysis (MAGeCK-style)
A pure-Python pipeline for CRISPR screen analysis with robust rank aggregation and essential gene identification.
- sgRNA count normalization (median ratio method)
- Gene-level score aggregation (Robust Rank Aggregation, RRA)
- Essential gene identification (dropout analysis)
- Pathway enrichment of screen hits (Fisher's exact test)
- Screen quality metrics (Gini index, ROC for known essentials)
- 20,000 sgRNAs × 4 samples (4000 genes, 5 sgRNAs/gene)
- Depleted genes (FDR<0.05): 202
- Enriched genes (FDR<0.05): 57
- Essential gene recovery: 200/200 (100%)
- ROC AUC: 1.000
pip install numpy scipy matplotlib
python crispr_screen_engine.pycrispr-screen sgrna mageck gene-essentiality dropout-analysis functional-genomics