Harman

DOI: 10.18129/B9.bioc.Harman    

This package is for version 3.15 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: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	IntroductionToHarman
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription
Version	1.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 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
SystemRequirements
Enhances
URL	http://www.bioinformatics.csiro.au/harman/
Depends On Me
Imports Me	debrowser
Suggests Me	HarmanData
Links To Me
Build Report

Package Archives

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

Source Package	Harman_1.24.0.tar.gz
Windows Binary	Harman_1.24.0.zip (64-bit only)
macOS Binary (x86_64)	Harman_1.24.0.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