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BERT

This is the development version of BERT; to use it, please install the devel version of Bioconductor.

Hierarchical Batch-Effect Adjustment with Trees


Bioconductor version: Development (3.19)

Provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Author: Yannis Schumann [aut, cre] , Simon Schlumbohm [aut]

Maintainer: Yannis Schumann <schumany at hsu-hh.de>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BERT")

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("BERT")
BERT-Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, ExperimentalDesign, Preprocessing, Software
Version 0.99.16
In Bioconductor since BioC 3.19 (R-4.4)
License GPL-3
Depends R (>= 4.3.0)
Imports cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators (>= 1.0.14), janitor (>= 2.2.0), limma(>= 3.46.0), logging (>= 0.10-108), sva(>= 3.38.0), SummarizedExperiment, methods, BiocParallel
System Requirements
URL https://github.com/HSU-HPC/BERT/
Bug Reports https://github.com/HSU-HPC/BERT/issues
See More
Suggests testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
Linking To
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 BERT_0.99.16.tar.gz
Windows Binary BERT_0.99.16.zip
macOS Binary (x86_64) BERT_0.99.16.tgz
macOS Binary (arm64) BERT_0.99.16.tgz
Source Repository git clone https://git.bioconductor.org/packages/BERT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BERT
Bioc Package Browser https://code.bioconductor.org/browse/BERT/
Package Short Url https://bioconductor.org/packages/BERT/
Package Downloads Report Download Stats