BEclear

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

Correction of batch effects in DNA methylation data

Bioconductor version: Release (3.23)

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: 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")):

Livia Rasp, Markus Merl, Ruslan Akulenko. BEclear: Correction of batch effects in DNA methylation data. doi:10.18129/B9.bioc.BEclear, R package version 2.28.0, https://bioconductor.org/packages/BEclear.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	2.28.0
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	GPL-3
Depends	BiocParallel (>= 1.14.2)
Imports	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
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	BEclear_2.28.0.tar.gz
Windows Binary (x86_64)	BEclear_2.28.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	BEclear_2.28.0.tgz
macOS Binary (sonoma-arm64)	BEclear_2.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BEclear
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BEclear
Package Short Url	https://bioconductor.org/packages/BEclear/
Package Downloads Report	Download Stats