BEclear
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BEclear.
Correction of batch effects in DNA methylation data
Bioconductor version: 3.10
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("BEclear")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, DNAMethylation, Preprocessing, Software, StatisticalMethod |
| Version | 2.2.0 |
| 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, outliers, abind, stats, graphics, utils, methods |
| System Requirements | C++11 |
| URL | https://github.com/David-J-R/BEclear |
| Bug Reports | https://github.com/David-J-R/BEclear/issues |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, pander |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BEclear_2.2.0.tar.gz |
| Windows Binary | BEclear_2.2.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | BEclear_2.2.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |