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

Handles missing values and makes more data available

Bioconductor version: Development (3.20)

An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.

Author: Simon Schlumbohm [aut, cre], Julia Neumann [aut], Philipp Neumann [aut]

Maintainer: Simon Schlumbohm <schlumbohm at>

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


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:

HarmonizR_Vignette HTML R Script
Reference Manual PDF


biocViews BatchEffect, Software
Version 1.3.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License GPL-3
Depends R (>= 4.2.0)
Imports doParallel (>= 1.0.16), foreach (>= 1.5.1), janitor (>= 2.1.0), plyr (>= 1.8.6), sva(>= 3.36.0), seriation (>= 1.3.5), limma(>= 3.46.0), SummarizedExperiment
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Suggests knitr, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package HarmonizR_1.3.0.tar.gz
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macOS Binary (x86_64) HarmonizR_1.3.0.tgz
macOS Binary (arm64) HarmonizR_1.3.0.tgz
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Source Repository (Developer Access) git clone
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