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BEclear

Correction of batch effects in DNA methylation data


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("BEclear")):

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

Details

biocViews BatchEffect, DNAMethylation, Preprocessing, Software, StatisticalMethod
Version 2.18.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
System Requirements C++11
URL https://github.com/uds-helms/BEclear
Bug Reports https://github.com/uds-helms/BEclear/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, pander, seewave
Linking To Rcpp
Enhances
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Package Archives

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

Source Package BEclear_2.18.0.tar.gz
Windows Binary BEclear_2.18.0.zip
macOS Binary (x86_64) BEclear_2.18.0.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