Package: BEclear 2.23.0

Livia Rasp

BEclear: Correction of batch effects in DNA methylation data

Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Authors:Livia Rasp [aut, cre], Markus Merl [aut], Ruslan Akulenko [aut]

BEclear_2.23.0.tar.gz
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BEclear.pdf |BEclear.html
BEclear/json (API)
NEWS

# Install 'BEclear' in R:
install.packages('BEclear', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/uds-helms/beclear/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ex.corrected.data - Example matrix of corrected data for the BEclear-package
  • ex.data - Example data set for the BEclear-package
  • ex.samples - Example data set for the BEclear-package

On BioConductor:BEclear-2.23.0(bioc 3.21)BEclear-2.22.0(bioc 3.20)

batcheffectdnamethylationsoftwarepreprocessingstatisticalmethodbatch-effectsbioconductor-packagedna-methylationlatent-factor-modelmethylationmissing-datamissing-valuesstochastic-gradient-descentcpp

5.90 score 4 stars 11 scripts 372 downloads 3 mentions 13 exports 22 dependencies

Last updated 5 months agofrom:4a3e2f429e. Checks:1 OK, 10 NOTE, 1 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-win-x86_64NOTEMar 29 2025
R-4.5-mac-x86_64NOTEMar 29 2025
R-4.5-mac-aarch64NOTEMar 29 2025
R-4.5-linux-x86_64NOTEMar 29 2025
R-4.4-win-x86_64NOTEMar 29 2025
R-4.4-mac-x86_64NOTEMar 29 2025
R-4.4-mac-aarch64NOTEMar 29 2025
R-4.4-linux-x86_64NOTEMar 29 2025
R-4.3-win-x86_64NOTEMar 29 2025
R-4.3-mac-x86_64NOTEMar 29 2025
R-4.3-mac-aarch64ERRORMar 29 2025

Exports:calcBatchEffectscalcScorecalcSummaryclearBEgenescorrectBatchEffectcountValuesToPredictfindOutsideValuesimputeMissingDatalocalLosslossmakeBoxplotpreprocessBEclearreplaceOutsideValues

Dependencies:abindaskpassBHBiocParallelcodetoolscpp11data.tabledixonTestformatRfutile.loggerfutile.optionsidslambda.rlatticeMatrixopensslrbibutilsRcppRdpacksnowsysuuid

Detecting and correcting batch effects with BEclear

Rendered fromBEclear.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2023-04-06
Started: 2018-12-07