Bioconductor – Harman

DOI: 10.18129/B9.bioc.Harman  

 

This package is for version 3.12 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: 3.12

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")):

Installation

To install this package, start R (version
“4.0”) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Harman")

For older versions of R, please refer to the appropriate
Bioconductor release.

Documentation

To view documentation for the version of this package installed
in your system, start R and enter:

browseVignettes("Harman")

 

Details

biocViews BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription
Version 1.18.0
In Bioconductor since BioC 3.3 (R-3.3) (5 years)
License GPL-3 + file LICENCE
Depends R (>= 3.6)
Imports Rcpp (>= 0.11.2), graphics, stats, methods
LinkingTo Rcpp
Suggests HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva
SystemRequirements
Enhances
URL www.bioinformatics.csiro.au/harman/
BugReports github.com/JasonR055/Harman/issues
Depends On Me
Imports Me debrowser
Suggests Me
Links To Me
Build Report  

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