To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Harman")

In most cases, you don't need to download the package archive at all.

Harman

This package is for version 3.4 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: 3.4

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Harman")

Documentation

HTML R Script IntroductionToHarman
PDF Reference Manual
Text NEWS

Details

biocViews BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription
Version 1.2.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
License GPL-3 + file LICENCE
Depends R (>= 3.3)
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
SystemRequirements
Enhances
URL http://www.bioinformatics.csiro.au/harman/
BugReports https://github.com/JasonR055/Harman/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source Harman_1.2.0.tar.gz
Windows Binary Harman_1.2.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) Harman_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/Harman/tree/release-3.4
Package Short Url http://bioconductor.org/packages/Harman/
Package Downloads Report Download Stats

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