beer
This is the released version of beer; for the devel version, see beer.
Bayesian Enrichment Estimation in R
Bioconductor version: Release (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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.15.1 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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_1.15.1.tar.gz |
| Windows Binary (x86_64) | beer_1.15.1.zip |
| macOS Binary (big-sur-x86_64) | beer_1.15.1.tgz |
| macOS Binary (sonoma-arm64) | beer_1.15.1.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 |