bio-crispr-screens-bagel-essentiality

Name: bio-crispr-screens-bagel-essentiality
Rating: 5 (1 reviews)
Author: bg-szy

Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement

1stars

Updated 18 days ago

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Version Compatibility

Reference examples tested with: BAGEL2 1.0.5+ (hart-lab/bagel), pandas 2.2+, numpy 1.26+, scipy 1.12+, matplotlib 3.8+.

Before using code patterns, verify installed versions match. If versions differ:

CLI: BAGEL.py fc --help; BAGEL.py bf --help; BAGEL.py pr --help
Python: BAGEL2 is distributed via git clone (no canonical PyPI release); confirm python BAGEL.py --version after checkout.