addFeature	addFeature-methods
addFeature,ChipDataSet-method	addFeature-methods
annot	annot
annotateTranscripts	annotateTranscripts-methods
annotateTranscripts,TranscriptionDataSet,GRanges-method	annotateTranscripts-methods
breakTranscriptsByPeaks	breakTranscriptsByPeaks-methods
breakTranscriptsByPeaks,TranscriptionDataSet,ChipDataSet-method	breakTranscriptsByPeaks-methods
cds	cds
ChipDataSet	ChipDataSet-class
ChipDataSet-class	ChipDataSet-class
constructCDS	constructCDS
constructTDS	constructTDS
detectTranscripts	detectTranscripts-methods
detectTranscripts,TranscriptionDataSet-method	detectTranscripts-methods
estimateBackground	estimateBackground-methods
estimateBackground,TranscriptionDataSet-method	estimateBackground-methods
estimateGapDistance	estimateGapDistance-methods
estimateGapDistance,TranscriptionDataSet,GRanges-method	estimateGapDistance-methods
exportCoverage	exportCoverage-methods
exportCoverage,TranscriptionDataSet-method	exportCoverage-methods
getConfusionMatrix	getConfusionMatrix-methods
getConfusionMatrix,ChipDataSet-method	getConfusionMatrix-methods
getGenomicAnnot	getGenomicAnnot-methods
getGenomicAnnot,ChipDataSet-method	getGenomicAnnot-methods
getPeaks	getPeaks-methods
getPeaks,ChipDataSet-method	getPeaks-methods
getPredictorSignificance	getPredictorSignificance-methods
getPredictorSignificance,ChipDataSet-method	getPredictorSignificance-methods
getProbTreshold	getProbTreshold-methods
getProbTreshold,ChipDataSet-method	getProbTreshold-methods
getQuadProb	getQuadProb-methods
getQuadProb,ChipDataSet-method	getQuadProb-methods
getTestedGapDistances	getTestedGapDistances-methods
getTestedGapDistances,TranscriptionDataSet-method	getTestedGapDistances-methods
getTranscripts	getTranscripts-methods
getTranscripts,TranscriptionDataSet-method	getTranscripts-methods
peaksToBed	peaksToBed-methods
peaksToBed,ChipDataSet-method	peaksToBed-methods
plotErrorRate	plotErrorRate-methods
plotErrorRate,TranscriptionDataSet-method	plotErrorRate-methods
plotFeatures	plotFeatures-methods
plotFeatures,ChipDataSet-method	plotFeatures-methods
plotGenomicAnnot	plotGenomicAnnot-methods
plotGenomicAnnot,ChipDataSet-method	plotGenomicAnnot-methods
plotROC	plotROC-methods
plotROC,ChipDataSet-method	plotROC-methods
predictStrand	predictStrand-methods
predictStrand,ChipDataSet,TranscriptionDataSet-method	predictStrand-methods
predictTssOverlap	predictTssOverlap-methods
predictTssOverlap,ChipDataSet-method	predictTssOverlap-methods
show	show
show,ChipDataSet-method	show
show,TranscriptionDataSet-method	show
tds	tds
TranscriptionDataSet	TranscriptionDataSet-class
TranscriptionDataSet-class	TranscriptionDataSet-class
transcriptsToBed	transcriptsToBed-methods
transcriptsToBed,GRanges-method	transcriptsToBed-methods
