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 | 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 |