HarmonizR

DOI: 10.18129/B9.bioc.HarmonizR  

Handles missing values and makes more data available

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>

Installation

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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HarmonizR")

 

HTML	R Script	HarmonizR_Vignette
PDF		Reference Manual
Text		NEWS

Details

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

Package Archives

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