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Data & Repro
BI
bio-crispr-screens-mageck-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis. Use when identifying essential genes, drug targets, or resistance mechanisms from dropout or enrichment screens.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-crispr-screens-mageck-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: mageck count → mageck test for standard analysis.
- CLI: mageck mle for multi-condition designs.
- Analyze my pooled CRISPR screen with MAGeCK" → Count sgRNA reads, normalize across samples, and rank genes by enrichment or depletion using the MAGeCK robust rank aggregation algorithm. CLI: mageck count → mageck test for standard analysis CLI: mageck mle for multi-condition designs.
- mageck count \ -l library.csv \ -n experiment \ --sample-label Day0,Treated1,Treated2,Control1,Control2 \ --fastq Day0.fastq.gz Treated1.fastq.gz Treated2.fastq.gz Control1.fastq.gz Control2.fastq.gz \ --norm-method median.
Source Doc
Excerpt From SKILL.md
Count sgRNAs from FASTQ
Goal: Quantify sgRNA representation from raw sequencing data.
Approach: Map FASTQ reads to the sgRNA library sequences with MAGeCK count, producing a normalized count matrix and QC summary across all samples.
## library.csv (tab-separated)
sgRNA_ID Gene Sequence
BRCA1_1 BRCA1 ATGGATTTATCTGCTCTTCG
BRCA1_2 BRCA1 CAGCAGATACTTGATGCATC
TP53_1 TP53 CCATTGTTCAATATCGTCCG
...
MAGeCK Test (RRA Algorithm)
Goal: Identify genes significantly enriched or depleted between treatment and control conditions.
Approach: Run MAGeCK test with robust rank aggregation, which ranks sgRNAs by fold change, tests whether per-gene sgRNA rankings deviate from uniform, and reports gene-level significance with FDR correction.
Use cases
- Use when identifying essential genes, drug targets, or resistance mechanisms from dropout or enrichment screens.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- screen-qc - Quality control before MAGeCK
- hit-calling - Alternative hit calling methods
- pathway-analysis/gsea - Downstream enrichment analysis
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