An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification


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Documentation for package ‘transcriptR’ version 1.4.0

Help Pages

addFeature addFeature
addFeature-method addFeature
annot Reference annotation (knownGene from UCSC)
annotateTranscripts annotateTranscripts
annotateTranscripts-method annotateTranscripts
breakTranscriptsByPeaks breakTranscriptsByPeaks
breakTranscriptsByPeaks-method breakTranscriptsByPeaks
cds Example of 'ChipDataSet' object.
ChipDataSet ChipDataSet
ChipDataSet-class ChipDataSet
constructCDS constructCDS
constructTDS constructTDS
detectTranscripts detectTranscripts
detectTranscripts-method detectTranscripts
estimateBackground estimateBackground
estimateBackground-method estimateBackground
estimateGapDistance estimateGapDistance
estimateGapDistance-method estimateGapDistance
exportCoverage exportCoverage
exportCoverage-method exportCoverage
getConfusionMatrix getConfusionMatrix
getConfusionMatrix-method getConfusionMatrix
getGenomicAnnot getGenomicAnnot
getGenomicAnnot-method getGenomicAnnot
getPeaks getPeaks
getPeaks-method getPeaks
getPredictorSignificance getPredictorSignificance
getPredictorSignificance-method getPredictorSignificance
getProbTreshold getProbTreshold
getProbTreshold-method getProbTreshold
getQuadProb getQuadProb
getQuadProb-method getQuadProb
getTestedGapDistances getTestedGapDistances
getTestedGapDistances-method getTestedGapDistances
getTranscripts getTranscripts
getTranscripts-method getTranscripts
peaksToBed peaksToBed
peaksToBed-method peaksToBed
plotErrorRate plotErrorRate
plotErrorRate-method plotErrorRate
plotFeatures plotFeatures
plotFeatures-method plotFeatures
plotGenomicAnnot plotGenomicAnnot
plotGenomicAnnot-method plotGenomicAnnot
plotROC plotROC
plotROC-method plotROC
predictStrand predictStrand
predictStrand-method predictStrand
predictTssOverlap predictTssOverlap
predictTssOverlap-method predictTssOverlap
show Show method for ChipDataSet and TranscriptionDataSet objects
show-method Show method for ChipDataSet and TranscriptionDataSet objects
tds Example of 'TranscriptionDataSet' object.
TranscriptionDataSet TranscriptionDataSet
TranscriptionDataSet-class TranscriptionDataSet
transcriptsToBed transcriptsToBed
transcriptsToBed-method transcriptsToBed