BEclear

This is the released version of BEclear; for the devel version, see BEclear.

Correction of batch effects in DNA methylation data

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DOI: 10.18129/B9.bioc.BEclear

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0003-0164-2163 , 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, DNAMethylation, Preprocessing, Software, StatisticalMethod

Version 2.26.0

In Bioconductor since BioC 3.1 (R-3.2) (10.5 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

System Requirements C++11

URL https://github.com/uds-helms/BEclear

Bug Reports https://github.com/uds-helms/BEclear/issues

Suggests testthat, BiocStyle, knitr, rmarkdown, pander, seewave

Linking To Rcpp

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package BEclear_2.26.0.tar.gz

Windows Binary (x86_64) BEclear_2.25.0.zip (64-bit only)

macOS Binary (x86_64) BEclear_2.26.0.tgz

macOS Binary (arm64) BEclear_2.26.0.tgz

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/

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