HarmonizR
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see HarmonizR.
Handles missing values and makes more data available
Bioconductor version: 3.19
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("HarmonizR")):
Installation
To install this package, start R (version "4.4") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HarmonizR")| HarmonizR_Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HarmonizR_1.2.0.tar.gz |
| Windows Binary (x86_64) | HarmonizR_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | HarmonizR_1.2.0.tgz |
| macOS Binary (arm64) | HarmonizR_1.2.0.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 |