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Brundle
View on CRAN: Click
here
Download and install Brundle package within the R console
Install from CRAN:
install.packages("Brundle")
Install from Github:
library("remotes")
install_github("cran/Brundle") Install by package version:
library("remotes")
install_version("Brundle", "1.0.9") Attach the package and use:
library("Brundle")
Maintained by
Andrew N Holding
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-09-19
Latest Update:
Description:
Inter-sample condition variability is a key challenge of normalising ChIP-seq data. This implementation uses either spike-in or a second factor as a control for normalisation. Input can either be from 'DiffBind' or a matrix formatted for 'DESeq2'. The output is either a 'DiffBind' object or the default 'DESeq2' output. Either can then be processed as normal. Supporting manuscript Guertin, Markowetz and Holding (2017) .
How to cite:
Andrew N Holding (2017). Brundle: Normalisation Tools for Inter-Condition Variability of ChIP-Seq
Data. R package version 1.0.9, https://cran.r-project.org/web/packages/Brundle. Accessed 05 Jun. 2026.
Previous versions and publish date:
Other packages that cited Brundle R package
View Brundle citation profile
Other R packages that Brundle depends,
imports, suggests or enhances
Functions, R codes and Examples using
the Brundle R package
Some associated functions: Brundle . dbaControl . dbaExperiment . jg.applyNormalisation . jg.conditions . jg.controlCountsTreated . jg.controlCountsUntreated . jg.controlPeaks . jg.controlPeakset . jg.controlPeaksetDeSeq . jg.controlResultsDeseq . jg.convertPeakset . jg.correctDBASizeFactors . jg.countAlignedMReads . jg.dbaGetPeakset . jg.experimentPeakset . jg.experimentResultsDeseq . jg.getControlCounts . jg.getCorrectionFactor . jg.getDba . jg.getNormalizationCoefficient . jg.getSampleIds . jg.plotDeSeq . jg.plotDeSeqCombined . jg.plotMA . jg.plotNormalization . jg.runDeSeq .
Some associated R codes: brundle-data.R . brundle.R . Full Brundle package functions and examples
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