BEclear

DOI: 10.18129/B9.bioc.BEclear  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BEclear.

Correction of batch effects in DNA methylation data

Bioconductor version: 3.16

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: David Rasp [aut, cre] , Markus Merl [aut], Ruslan Akulenko [aut]

Maintainer: David Rasp <david.j.rasp at gmail.com>

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

Installation

To install this package, start R (version "4.2") 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 2.14.0
In Bioconductor since BioC 3.1 (R-3.2) (8 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_2.14.0.tar.gz
Windows Binary BEclear_2.14.0.zip (64-bit only)
macOS Binary (x86_64) BEclear_2.14.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: