BERT

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

High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT)

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DOI: 10.18129/B9.bioc.BERT

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-2379-200X , Simon Schlumbohm [aut] ORCID iD ORCID: 0000-0002-0083-5142

Maintainer: Yannis Schumann <yannis.schumann at desy.de>

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

Installation

To install this package, start R (version "4.5") and enter:


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, ExperimentalDesign, Preprocessing, QualityControl, Software

Version 1.6.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

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

Suggests testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle

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Package Archives

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

Source Package BERT_1.6.0.tar.gz

Windows Binary (x86_64) BERT_1.5.0.zip

macOS Binary (x86_64) BERT_1.6.0.tgz

macOS Binary (arm64) BERT_1.6.0.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/

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