beer
Bioc currentBayesian Enrichment Estimation in R
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
31 10 exported
Complexity
4.1 avg / 14 max
Call network
31 nodes / 38 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
4,527
Files
67
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
21
Testing
Has tests
Yes
Test-to-code ratio
0.30
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
1 externalJAGS (4.3.0)
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-04-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 32 (1 internal)includes a package overview page
- Examples that run
- 100%10 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 76%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- beer HTML
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/athchen/beer on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows
Datasets
Topics
People
- Athena Chen author maintainer
- Ingo Ruczinski author
- Rob Scharpf author
Cite
Cite this package
Run in R for the authors' entry:
citation("beer")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.