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Bioconductor - Harman (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription Version 1.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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.

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