DOI: 10.18129/B9.bioc.Harman    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see Harman.

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

Bioconductor version: 3.10

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

Maintainer: Jason Ross <jason.ross at csiro.au>

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


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biocViews BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription
Version 1.14.0
In Bioconductor since BioC 3.3 (R-3.3) (4 years)
License GPL-3 + file LICENCE
Depends R (>= 3.5)
Imports Rcpp (>= 0.11.2), graphics, stats
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/
BugReports https://github.com/JasonR055/Harman/issues
Depends On Me
Imports Me debrowser
Suggests Me
Links To Me
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Source Package Harman_1.14.0.tar.gz
Windows Binary Harman_1.14.0.zip
Mac OS X 10.11 (El Capitan) Harman_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Harman
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Harman
Package Short Url https://bioconductor.org/packages/Harman/
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