Harman
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Bioconductor version: Release (3.20)
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("Harman")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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/ |
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.
| Source Package | Harman_1.34.0.tar.gz |
| Windows Binary (x86_64) | Harman_1.34.0.zip |
| macOS Binary (x86_64) | Harman_1.34.0.tgz |
| macOS Binary (arm64) | Harman_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Harman |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Harman |
| Bioc Package Browser | https://code.bioconductor.org/browse/Harman/ |
| Package Short Url | https://bioconductor.org/packages/Harman/ |
| Package Downloads Report | Download Stats |