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Harman

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

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


Bioconductor version: Development (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 csiro.au>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
IntroductionToHarman HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription
Version 1.31.0
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
URL http://www.bioinformatics.csiro.au/harman/
See More
Suggests HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva
Linking To Rcpp
Enhances
Depends On Me
Imports Me debrowser
Suggests Me HarmanData
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Harman_1.31.0.tar.gz
Windows Binary Harman_1.31.0.zip
macOS Binary (x86_64) Harman_1.31.0.tgz
macOS Binary (arm64) Harman_1.31.0.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/
Package Downloads Report Download Stats