MAGeCK pooled-screen analysis

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 enrichment/depletion. This workflow analyzes screens; it does not design guides or infer gene function from a hit alone.

Runtime

The tested source installation and external-runtime caveat are in references/runtime.md. Verify both mageck --version and mageck test --help before an analysis. The bundled Python helper is standard-library only. MAGeCK itself also needs NumPy, SciPy, and the RRA binary. PDF/R reporting is optional and not needed by the helper.