bio-crispr-screens-mageck-analysis
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-crispr-screens-mageck-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: MAGeCK 0.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # MAGeCK CRISPR Screen Analysis **"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 ## 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. ```bash # Count reads mapping to sgRNA library mageck count \ -l library.csv \ -n experiment \ --sample-label Day0,Treated1,Treat
- Version Compatibility
- Count sgRNAs from FASTQ
- Library File Format
- MAGeCK Test (RRA Algorithm)
- MAGeCK MLE (Maximum Likelihood)
- Interpret Results
- Visualize Results
- MAGeCK Pathway Analysis
- Time-Course Screens
- CRISPR Activation (CRISPRa) Screens
- MAGeCK-VISPR (Visualization)
- Related Skills
Count reads mapping to sgRNA library mageck count \ Output files: experiment.count.txt - normalized counts experiment.count_normalized.txt - normalized counts experiment.countsummary.txt - QC summary Compare treatment vs control mageck test \ results.gene_summary.txt - gene-level results results.sgrna_summary.txt - sgRNA-level results
What does the bio-crispr-screens-mageck-analysis skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-crispr-screens-mageck-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.