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Bioconductor - beer

beer

This is the released version of beer; for the devel version, see beer.

Bayesian Enrichment Estimation in R

Bioconductor version: Release (3.21)

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 (from within R, enter 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 appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("beer")
Details biocViews Bayesian, Coverage, Sequencing, Software, StatisticalMethod Version 1.12.0 In Bioconductor since BioC 3.15 (R-4.2) (3 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 Package Archives

Follow Installation instructions to use this package in your R session.

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