beer

DOI: 10.18129/B9.bioc.beer  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see beer.

Bayesian Enrichment Estimation in R

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	beer
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, Coverage, Sequencing, Software, StatisticalMethod
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.2.0), PhIPData(>= 1.1.1), rjags
Imports	cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils
LinkingTo
Suggests	testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling
SystemRequirements	JAGS (4.3.0)
Enhances
URL	https://github.com/athchen/beer/
BugReports	https://github.com/athchen/beer/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	beer_1.2.0.tar.gz
Windows Binary	beer_1.2.0.zip
macOS Binary (x86_64)	beer_1.2.0.tgz
macOS Binary (arm64)	beer_1.2.0.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