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HarmonizR

This is the development version of HarmonizR; for the stable release version, see HarmonizR.

Handles missing values and makes more data available


Bioconductor version: Development (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 (from within R, enter citation("HarmonizR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews BatchEffect, Software
Version 1.1.0
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
System Requirements
URL
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Suggests knitr, rmarkdown, testthat (>= 3.0.0)
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HarmonizR_1.1.0.tar.gz
Windows Binary HarmonizR_1.1.0.zip
macOS Binary (x86_64) HarmonizR_1.1.0.tgz
macOS Binary (arm64) HarmonizR_1.1.0.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