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The removal of batch effects from datasets using a PCA and constrained optimisation based technique

Bioconductor version: Release (3.19)

Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.

Author: Yalchin Oytam [aut], Josh Bowden [aut], Jason Ross [aut, cre]

Maintainer: Jason Ross <jason.ross at>

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


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:

IntroductionToHarman HTML R Script
Reference Manual PDF


biocViews BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription
Version 1.32.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3 + file LICENCE
Depends R (>= 3.6)
Imports Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats
System Requirements
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Suggests HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva
Linking To Rcpp
Depends On Me
Imports Me debrowser
Suggests Me HarmanData
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package Harman_1.32.0.tar.gz
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macOS Binary (x86_64) Harman_1.32.0.tgz
macOS Binary (arm64) Harman_1.32.0.tgz
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Source Repository (Developer Access) git clone
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