Data & ReproStatistics & Data AnalysisFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-crispr-screens-hit-calling

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-crispr-screens-hit-calling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epidemiological & causal genomicsstatistical

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-crispr-screens-hit-calling

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: BAGEL.py bf for Bayes factor essentiality scoring.
Python: drugZ for fold-change based analysis.
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 fc \ -i counts.txt \ -o foldchange.txt \ -c Control1,Control2 \ -t Treatment1,Treatment2.

Source Doc

Excerpt From SKILL.md

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.


## Calculate Bayes Factor

bagel2 bf \
    -i foldchange.txt \
    -o bayes_factor.txt \
    -e essential_genes.txt \
    -n nonessential_genes.txt \
    -c 1  # Number of bootstrap iterations

## Precision-recall analysis

bagel2 pr \
    -i bayes_factor.txt \
    -o precision_recall.txt \
    -e essential_genes.txt \
    -n nonessential_genes.txt