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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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/ |
| Package Downloads Report | Download Stats |