beer
This is thereleased version of beer; for the devel version, seebeer.
Bayesian Enrichment Estimation in R
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0001-6900-2264, Rob Scharpf [aut], Ingo Ruczinski [aut]
Maintainer: Athena Chen <achen70 at jhu.edu>
citation("beer")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("beer")For older versions of R, please refer to the appropriateBioconductor 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 | 1.14.1 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 years) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | beer_1.14.1.tar.gz |
| Windows Binary (x86_64) | beer_1.14.1.zip (64-bit only) |
| macOS Binary (x86_64) | beer_1.14.1.tgz |
| macOS Binary (arm64) | beer_1.14.1.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 |
| Old Source Packages for BioC 3.22 | Source Archive |