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bio-crispr-screens-jacks-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR screens simultaneously or when accounting for variable sgRNA efficiency across experiments.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-crispr-screens-jacks-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: jacks.infer_JACKS() for joint analysis across experiments.
- Analyze multiple CRISPR screens jointly with JACKS" → Model sgRNA efficacy and gene essentiality simultaneously across multiple screens, accounting for variable guide efficiency. Python: jacks.infer_JACKS() for joint analysis across experiments.
- JACKS jointly models sgRNA efficacy and gene essentiality across multiple experiments. It infers both gene-level fitness effects and sgRNA-specific efficiency.
- git clone https://github.com/felicityallen/JACKS.git cd JACKS && pip install -e.
Source Doc
Excerpt From SKILL.md
counts.txt (tab-separated)
sgRNA Gene Sample1 Sample2 Sample3 Control1 Control2 sgRNA1 GENE_A 100 120 90 80 85 sgRNA2 GENE_A 200 180 210 150 160 sgRNA3 GENE_B 50 45 55 60 58 ...
## replicatemap.txt
Sample1 Experiment1 Day14
Sample2 Experiment1 Day14
Sample3 Experiment2 Day14
Control1 Experiment1 Day0
Control2 Experiment2 Day0
guidemap.txt
sgRNA1 GENE_A sgRNA2 GENE_A sgRNA3 GENE_B sgRNA4 GENE_B ...
Use cases
- Use when analyzing multiple CRISPR screens simultaneously or when accounting for variable sgRNA efficiency across experiments.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- mageck-analysis - Alternative screen analysis method
- hit-calling - Statistical hit identification
- screen-qc - Quality control before analysis
- batch-correction - Handle batch effects in multi-screen data
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