BAGEL specifications


Unique identifier OMICS_19070
Alternative name Bayesian Analysis of Gene EssentiaLity
Software type Framework/Library
Interface Command line interface, Application programming interface
Restrictions to use None
Input format TXT
Output format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 0.9
Stability Stable
numpy, scipy
Maintained Yes


No version available


  • person_outline Traver Hart

Publication for Bayesian Analysis of Gene EssentiaLity

BAGEL citations


Toward an integrated map of genetic interactions in cancer cells

Mol Syst Biol
PMCID: 5820685
PMID: 29467179
DOI: 10.15252/msb.20177656

[…] nch et al, ; Munoz et al, ), no read count data were available. Here, we used the original fold change values provided by the authors of the experiments.In order to assess the quality of each screen, Bayesian Analysis of Gene Essentiality (BAGEL; Hart & Moffat, ) was used to predict gene essentiality. Using precision–recall curves the ability to separate core‐essential and non‐essential genes base […]


Evaluation and Design of Genome Wide CRISPR/SpCas9 Knockout Screens

PMCID: 5555476
PMID: 28655737
DOI: 10.1534/g3.117.041277

[…] .5 reads was added to all readcounts to prevent discontinuities from zeros. gRNA with <30 reads at the T0 timepoint were excluded from the fold-change calculation.Fold-changes were processed with the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm (), using the essential and nonessential training sets defined in . The resulting Bayes Factors (BFs) for all screens are included in Supplemen […]

BAGEL institution(s)
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Donnelly Centre, University of Toronto, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada

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