R Observatory: Metrics for BEclear version 2.28.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BEclear

Bioc current

Correction of batch effects in DNA methylation data

v2.28.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.1 · Apr 17, 2015

Current · Requires R 4.6

1.0 In 23 of 49 releases 3.23

Description

Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

23 13 exported

Complexity

5.4 avg / 32 max

Call network

23 nodes / 17 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

4,271

Files

76

Compiled share

1.6%

Has compiled src

Yes

Language breakdown

R 2,051 (48%)C/C++/src 70 (1.6%)Tests 517 (12.1%)Docs 1,299 (30.4%)Vignettes 334 (7.8%)

API

Exported functions

13

Internal functions

6

Recent export changes

v3.9+6 calcBatchEffects, findOutsideValues, localLoss +3 more −4 calcMedians, calcPvalues, findWrongValues 1 more

v3.8+1 imputeMissingData −1 BEclear

Testing & CI

Has tests

Yes

Test-to-code ratio

0.25

testthat edition

–

CI present

Yes

CI type

["travis"]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

15.4%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

1

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

23

First release

2015-04-16

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

17

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 163 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 92%
Return-value docs: 100%
References docs: 29%

Topics

Software › WorkflowStep › BatchEffect

Software › AssayDomain › DNAMethylation

Software

Software › WorkflowStep › Preprocessing

Software › StatisticalMethod

People

Livia Rasp author maintainer
Ruslan Akulenko author
Markus Merl author

At a glance

Version: 2.28.0
Category: software
License: GPL-3
Requires R: ≥ 4.6
Maintainer: Livia Rasp
Entered: 3.1 · Apr 17, 2015
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

BiocParallel (>= 1.14.2)Bioc

Imports

logger Rdpack Matrix data.table (>= 1.11.8)Rcpp abindstatsgraphicsutilsmethodsdixonTest ids

Suggests

testthatBiocStyleBiocknitr rmarkdown pander seewave

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BEclear")

Format

Rasp, L., Akulenko, R., & Merl, M. (2026). BEclear: Correction of batch effects in DNA methylation data (Version 2.28.0) [Computer software]. https://bioconductor.org/packages/BEclear

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for BEclear version 2.28.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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