BERT
Bioc currentHigh Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT)
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
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.
None published for Bioconductor
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 →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
3,533
Files
41
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
16
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.55
testthat edition
3
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
- Help pages
- 21
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- BERT-Vignette HTML
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/hsu-hpc/bert on 2026-10-21.
Topics
People
- Yannis Schumann author maintainer
- Simon Schlumbohm author
Cite
Cite this package
Run in R for the authors' entry:
citation("BERT")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1002/pmic.202400100.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.