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Hierarchical Batch-Effect Adjustment with Trees

Bioconductor version: Release (3.19)

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))


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 1.0.0
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_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) BERT_1.0.0.tgz
macOS Binary (arm64) BERT_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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