beer
Bayesian Enrichment Estimation in R
Bioconductor version: 3.23 · Package version: 1.15.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("beer")Details
| Maintainer | Athena Chen <achen70@jhu.edu> |
| Author | Athena Chen [aut, cre] (ORCID: <https://orcid.org/0000-0001-6900-2264>), Rob Scharpf [aut], Ingo Ruczinski [aut] |
| License | MIT + file LICENSE |
| URL | https://github.com/athchen/beer/ |
| Bug Reports | https://github.com/athchen/beer/issues |
| System Requirements | JAGS (4.3.0) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, Coverage, Sequencing, Software, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/beer/ |
Citation
From within R, enter citation("beer"):
Athena Chen, Rob Scharpf, Ingo Ruczinski. beer: Bayesian Enrichment Estimation in R. doi:10.18129/B9.bioc.beer, R package version 1.15.1, https://bioconductor.org/packages/beer.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | beer_1.15.1.tar.gz |
| Windows binary (x86_64) | beer_1.15.1.zip |
| macOS binary (arm64) | beer_1.15.1.tgz |
| macOS binary (x86_64) | beer_1.15.1.tgz |
Dependencies
Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags
Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils
Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling