Harman

This is the released version of Harman; for the devel version, see Harman.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

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

Bioconductor version: Release (3.23)

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")):

Yalchin Oytam, Josh Bowden, Jason Ross. Harman: The removal of batch effects from datasets using a PCA and constrained optimisation based technique. doi:10.18129/B9.bioc.Harman, R package version 1.40.0, https://bioconductor.org/packages/Harman.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

IntroductionToHarman	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription
Version	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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/

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	BatchQC, debrowser
Suggests Me	HarmanData
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	Harman_1.40.0.tar.gz
Windows Binary (x86_64)	Harman_1.40.0.zip
macOS Binary (big-sur-x86_64)	Harman_1.40.0.tgz
macOS Binary (sonoma-arm64)	Harman_1.40.0.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/
Package Downloads Report	Download Stats