Individual skill
mageck
Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces gene hit rankings with effect sizes and FDR. Use for new knockout, CRISPRi, or CRISPRa screen analysis, enrichment or depletion contrasts, and MAGeCK count/test workflows; existing public dependency-score lookup belongs to DepMap.
skills/mageck/SKILL.md
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- Last checked
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- License
- MIT
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- ai-scientist Repository topic
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SKILL.mdcore · 8,610 bytesSKILL.mdcore · 8,610 bytesSKILL.mdcore · 8,610 bytesreferences/design.mddoc · 2,996 bytesreferences/runtime.mddoc · 3,518 bytesscripts/screen_analysis.pyruns · 14,068 bytes
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# 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](references/runtime.md). Verify both `mageck --version` and
`mageck test --help` before an analysis. The bundled Python helper is standard-library only.