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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| IntroductionToHarman | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 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 | BatchQC, 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_1.41.0.tar.gz |
| Windows Binary (x86_64) | Harman_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | Harman_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | Harman_1.41.0.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 |