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This is the development version of BERT; for the stable release version, see BERT.

Hierarchical Batch-Effect Adjustment with Trees

Bioconductor version: Development (3.20)

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.

Author: Yannis Schumann [aut, cre] , Simon Schlumbohm [aut]

Maintainer: Yannis Schumann <schumany at>

Citation (from within R, enter citation("BERT")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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

BERT-Vignette HTML R Script
Reference Manual PDF


biocViews BatchEffect, ExperimentalDesign, Preprocessing, Software
Version 1.1.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3
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), SummarizedExperiment, methods, BiocParallel
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Suggests testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package BERT_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64) BERT_1.1.0.tgz
macOS Binary (arm64) BERT_1.1.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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