BERT
Hierarchical Batch-Effect Adjustment with Trees
Bioconductor version: Release (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")
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 | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, ExperimentalDesign, Preprocessing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (< 6 months) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | BERT_1.0.0.zip |
| macOS Binary (x86_64) | BERT_1.0.0.tgz |
| macOS Binary (arm64) | BERT_1.0.0.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/ |
| Package Downloads Report | Download Stats |