beer
This is the development version of beer; for the stable release version, see beer.
Bayesian Enrichment Estimation in R
Bioconductor version: Development (3.23)
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 "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("beer")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Bayesian, Coverage, Sequencing, Software, StatisticalMethod |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 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 | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/beer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/beer |
| Package Short Url | https://bioconductor.org/packages/beer/ |
| Package Downloads Report | Download Stats |