DOI: 10.18129/B9.bioc.Harman  

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

Bioconductor version: Release (3.17)

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 csiro.au>

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biocViews BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription
Version 1.28.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 years)
License GPL-3 + file LICENCE
Depends R (>= 3.6)
Imports Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats
LinkingTo Rcpp
Suggests HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva
URL http://www.bioinformatics.csiro.au/harman/
Depends On Me
Imports Me debrowser
Suggests Me HarmanData
Links To Me
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Source Package Harman_1.28.0.tar.gz
Windows Binary Harman_1.28.0.zip (64-bit only)
macOS Binary (x86_64) Harman_1.28.0.tgz
macOS Binary (arm64) Harman_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Harman
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Harman
Bioc Package Browser https://code.bioconductor.org/browse/Harman/
Package Short Url https://bioconductor.org/packages/Harman/
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