Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data


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Documentation for package ‘Brundle’ version 1.0.9

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Brundle Brundle
dbaControl Example DiffBind Object of Control Peaks
dbaExperiment Example DiffBind Object of Experimental Peaks
jg.applyNormalisation jg.applyNormalisation
jg.conditions Example Sample Condition Matrix
jg.controlCountsTreated Example ChIP-seq Count Matrix
jg.controlCountsUntreated Example ChIP-seq Count Matrix
jg.controlPeaks Example ChIP-seq Control Peakset
jg.controlPeakset Example ChIP-seq Control Peakset
jg.controlPeaksetDeSeq Example ChIP-seq Control Peakset
jg.controlResultsDeseq Example ChIP-seq DeSEQ2 Control results
jg.convertPeakset jg.convertPeakset
jg.correctDBASizeFactors jg.correctDBASizeFactors
jg.countAlignedMReads jg.countAlignedMReads
jg.dbaGetPeakset dbaGetPeakset
jg.experimentPeakset Example ChIP-seq Experiment Peakset
jg.experimentResultsDeseq Example ChIP-seq DeSEQ2 results
jg.getControlCounts jg.getControlCounts
jg.getCorrectionFactor jg.getCorrectionFactor
jg.getDba jg.getDba
jg.getNormalizationCoefficient jg.getNormalizationCoefficient
jg.getSampleIds jg.getSampleIds
jg.plotDeSeq jg.plotDeSeq
jg.plotDeSeqCombined jg.plotDeSeqCombined
jg.plotMA jg.plotMA
jg.plotNormalization jg.plotNormalization
jg.runDeSeq jg.runDeSeq