This package is for version 3.12 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: 3.12
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 (version
“4.0”) and enter:
if (!requireNamespace("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")
Details
biocViews | BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription |
Version | 1.18.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (5 years) |
License | GPL-3 + file LICENCE |
Depends | R (>= 3.6) |
Imports | Rcpp (>= 0.11.2), graphics, stats, methods |
LinkingTo | Rcpp |
Suggests | HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva |
SystemRequirements | |
Enhances | |
URL | www.bioinformatics.csiro.au/harman/ |
BugReports | github.com/JasonR055/Harman/issues |
Depends On Me | |
Imports Me | debrowser |
Suggests Me | |
Links To Me | |
Build Report |
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Installation instructions to use this
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