bio-crispr-screens-hit-calling
Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen count data after QC passes.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-crispr-screens-hit-calling --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+, scipy 1.12+, statsmodels 0.14+ 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. # CRISPR Screen Hit Calling **"Identify essential genes from my CRISPR screen"** → Call significant gene hits from sgRNA count data using statistical methods that account for guide-level variability and multiple testing. - CLI: `BAGEL.py bf` for Bayes factor essentiality scoring - Python: `drugZ` for fold-change based analysis ## BAGEL2 Analysis **Goal:** Identify essential genes using Bayesian classification against reference gene sets. **Approach:** Calculate sgRNA fold changes, compute Bayes Factors using known essential and non-essential gene sets as training data, and assess precision-recall at different thresholds. ```bash # BAGEL2 for Bayesian gene essentia
- Version Compatibility
- BAGEL2 Analysis
- DrugZ Analysis
- Custom Hit Calling in Python
- Robust Rank Aggregation (MAGeCK-style)
- Second-Best sgRNA Method
- Compare Methods
- Time-Course Analysis
- Visualize Results
- Related Skills
BAGEL2 for Bayesian gene essentiality Uses reference essential/non-essential genes Calculate fold changes bagel2 fc \ Calculate Bayes Factor bagel2 bf \ Precision-recall analysis bagel2 pr \ DrugZ for drug screens (synergy/resistance) drugz.py \
What does the bio-crispr-screens-hit-calling skill do?
Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen count data after QC passes.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-crispr-screens-hit-calling --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.