Harman
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Bioconductor version: 3.23 · Package version: 1.40.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Harman")Details
| Maintainer | Jason Ross <jason.ross@csiro.au> |
| Author | Yalchin Oytam [aut], Josh Bowden [aut], Jason Ross [aut, cre] |
| License | GPL-3 + file LICENCE |
| URL | http://www.bioinformatics.csiro.au/harman/ |
| Downloads rank | 642 |
| Source branch | RELEASE_3_23 |
| biocViews | BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | Harman_1.40.0.tar.gz |
| Windows binary (x86_64) | Harman_1.40.0.zip |
| macOS binary (arm64) | Harman_1.40.0.tgz |
| macOS binary (x86_64) | Harman_1.40.0.tgz |
Dependencies
Depends: R (>= 3.6)
Imports: Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats
LinkingTo: Rcpp
Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva