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beer

Bayesian Enrichment Estimation in R


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("beer")

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

Documentation

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

browseVignettes("beer")
beer HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Bayesian, Coverage, Sequencing, Software, StatisticalMethod
Version 1.6.0
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
See More
Suggests testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package beer_1.6.0.tar.gz
Windows Binary beer_1.6.0.zip (64-bit only)
macOS Binary (x86_64) beer_1.6.0.tgz
macOS Binary (arm64) beer_1.6.0.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/
Package Downloads Report Download Stats