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This is the development version of beer; for the stable release version, see beer.

Bayesian Enrichment Estimation in R

Bioconductor version: Development (3.19)

BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses.

Author: Athena Chen [aut, cre] , Rob Scharpf [aut], Ingo Ruczinski [aut]

Maintainer: Athena Chen <achen70 at jhu.edu>

Citation (from within R, enter citation("beer")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

beer HTML R Script
Reference Manual PDF


biocViews Bayesian, Coverage, Sequencing, Software, StatisticalMethod
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends R (>= 4.2.0), PhIPData(>= 1.1.1), rjags
Imports cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils
System Requirements JAGS (4.3.0)
URL https://github.com/athchen/beer/
Bug Reports https://github.com/athchen/beer/issues
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Suggests testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling
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Follow Installation instructions to use this package in your R session.

Source Package beer_1.7.0.tar.gz
Windows Binary beer_1.7.0.zip (64-bit only)
macOS Binary (x86_64) beer_1.7.0.tgz
macOS Binary (arm64) beer_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/beer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/beer
Bioc Package Browser https://code.bioconductor.org/browse/beer/
Package Short Url https://bioconductor.org/packages/beer/
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