Normalisation Tools for Inter-Condition Variability of ChIP-Seq
Data
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Documentation for package ‘Brundle’ version 1.0.9
Help Pages
| 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 |