BERT

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

Bioconductor version: 3.23 · Package version: 1.8.0

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.

Installation

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

BiocManager::install("BERT")

Details

Maintainer	Yannis Schumann <yannis.schumann@desy.de>
Author	Yannis Schumann [aut, cre] (ORCID: <https://orcid.org/0000-0002-2379-200X>), Simon Schlumbohm [aut] (ORCID: <https://orcid.org/0000-0002-0083-5142>)
License	GPL-3
URL	https://github.com/HSU-HPC/BERT/
Bug Reports	https://github.com/HSU-HPC/BERT/issues
Downloads rank	171
Source branch	RELEASE_3_23
biocViews	BatchEffect, ExperimentalDesign, Preprocessing, QualityControl, Software

Documentation

BERT-Vignette

Download

Source package

Dependencies

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

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