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Bioconductor version: Release (3.18)
An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.
Author: Simon Schlumbohm [aut, cre], Julia Neumann [aut], Philipp Neumann [aut]
Maintainer: Simon Schlumbohm <schlumbohm at hsu-hh.de>
Citation (from within R,
enter citation("HarmonizR")
):
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("HarmonizR")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HarmonizR")
HTML | R Script | HarmonizR_Vignette |
Reference Manual | ||
Text | NEWS |
biocViews | BatchEffect, Software |
Version | 1.0.0 |
In Bioconductor since | BioC 3.18 (R-4.3) (< 6 months) |
License | GPL-3 |
Depends | R (>= 4.2.0) |
Imports | doParallel (>= 1.0.16), foreach (>= 1.5.1), janitor (>= 2.1.0), plyr (>= 1.8.6), sva(>= 3.36.0), seriation (>= 1.3.5), limma(>= 3.46.0), SummarizedExperiment |
LinkingTo | |
Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | HarmonizR_1.0.0.tar.gz |
Windows Binary | HarmonizR_1.0.0.zip (64-bit only) |
macOS Binary (x86_64) | HarmonizR_1.0.0.tgz |
macOS Binary (arm64) | HarmonizR_1.0.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/HarmonizR |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HarmonizR |
Bioc Package Browser | https://code.bioconductor.org/browse/HarmonizR/ |
Package Short Url | https://bioconductor.org/packages/HarmonizR/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.18 | Source Archive |
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