BEclear

DOI: 10.18129/B9.bioc.BEclear  

Correction of batch effects in DNA methylation data

Bioconductor version: Release (3.17)

Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Author: Livia Rasp [aut, cre] , Markus Merl [aut], Ruslan Akulenko [aut]

Maintainer: Livia Rasp <livia.rasp at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("BEclear")

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("BEclear")

 

HTML	R Script	BEclear tutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BatchEffect, DNAMethylation, Preprocessing, Software, StatisticalMethod
Version	2.16.0
In Bioconductor since	BioC 3.1 (R-3.2) (8.5 years)
License	GPL-3
Depends	BiocParallel(>= 1.14.2)
Imports	futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids
LinkingTo	Rcpp
Suggests	testthat, BiocStyle, knitr, rmarkdown, pander, seewave
SystemRequirements	C++11
Enhances
URL	https://github.com/uds-helms/BEclear
BugReports	https://github.com/uds-helms/BEclear/issues
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	BEclear_2.16.0.tar.gz
Windows Binary	BEclear_2.16.0.zip (64-bit only)
macOS Binary (x86_64)	BEclear_2.16.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/BEclear
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BEclear
Bioc Package Browser	https://code.bioconductor.org/browse/BEclear/
Package Short Url	https://bioconductor.org/packages/BEclear/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive