R Observatory: Metrics for BERT version 1.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BERT

Bioc current

High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT)

v1.8.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.19 · May 1, 2024

Current · Requires R 4.6

1.0 In 5 of 49 releases 3.23

Description

Provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

21 5 exported

Complexity

7.8 avg / 24 max

Call network

21 nodes / 21 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

3,535

Files

46

Compiled share

0%

Has compiled src

No

Language breakdown

R 1,568 (44.4%)Tests 865 (24.5%)Docs 764 (21.6%)Vignettes 338 (9.6%)

API

Exported functions

5

Internal functions

16

Recent export changes

v3.19+5 BERT, compute_asw, count_existing +2 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.55

testthat edition

3

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

50%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.3.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

5

First release

2024-04-30

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

READMEYes · 380 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software › WorkflowStep › BatchEffect

Software › WorkflowStep › Preprocessing

Software › WorkflowStep › ExperimentalDesign

Software › WorkflowStep › QualityControl

People

Yannis Schumann author maintainer
Simon Schlumbohm author

At a glance

Version: 1.8.0
Category: software
License: GPL-3
Requires R: ≥ 4.6
Maintainer: Yannis Schumann
Entered: 3.19 · May 1, 2024
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 4.3.0)

Imports

cluster comprehenr foreach (>= 1.5.2)invgamma iterators (>= 1.0.14)janitor (>= 2.2.0)limma (>= 3.46.0)logging (>= 0.10-108)sva (>= 3.38.0)BiocSummarizedExperimentBiocmethodsBiocParallelBioc

Suggests

testthat (>= 3.0.0)knitr rmarkdownBiocStyleBioc

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BERT")

Format

Schumann, Y., & Schlumbohm, S. (2026). BERT: High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT) (Version 1.8.0) [Computer software]. https://bioconductor.org/packages/BERT

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 BERT version 1.8.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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