beer

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see beer.

Bayesian Enrichment Estimation in R

Bioconductor version: 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")):

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, Coverage, Sequencing, Software, StatisticalMethod

Version 1.8.0

In Bioconductor since BioC 3.15 (R-4.2) (2.5 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

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_1.8.0.tar.gz

Windows Binary (x86_64) beer_1.8.0.zip (64-bit only)

macOS Binary (x86_64) beer_1.8.0.tgz

macOS Binary (arm64) beer_1.8.0.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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