transite-package	transite
.RBPMotif	RBPMotif-class
.SpectrumScore	SpectrumScore-class
calculateKmerEnrichment	calculateKmerEnrichment
calculateKmerScores	calculateKmerScores
calculateLocalConsistency	calculateLocalConsistency
calculateMotifEnrichment	calculateMotifEnrichment
calculateTranscriptMC	calculateTranscriptMC
checkKmers	checkKmers
computeKmerEnrichment	computeKmerEnrichment
computeMotifScore	computeMotifScore
createKmerMotif	createKmerMotif
createMatrixMotif	createMatrixMotif
drawVolcanoPlot	drawVolcanoPlot
empiricalEnrichmentMeanCDF	empiricalEnrichmentMeanCDF
ge	ge
generateIUPACByKmers	generateIUPACByKmers
generateIUPACByMatrix	generateIUPACByMatrix
generateKmers	generateKmers
generateKmersFromIUPAC	generateKmersFromIUPAC
generatePermutedEnrichments	generatePermutedEnrichments
geometricMean	geometricMean
getMotifById	getMotifById
getMotifByRBP	getMotifByRBP
getMotifs	getMotifs
getPPM	getPPM
homopolymerCorrection	homopolymerCorrection
initIUPAClookupTable	initIUPAClookupTable
kmers.enrichment	kmers.enrichment
lookupKmerScores	lookupKmerScores
motifHeptamers	RBPMotif-class
motifHeptamers,RBPMotif-method	RBPMotif-class
motifHexamers	RBPMotif-class
motifHexamers,RBPMotif-method	RBPMotif-class
motifId	RBPMotif-class
motifId,RBPMotif-method	RBPMotif-class
motifIUPAC	RBPMotif-class
motifIUPAC,RBPMotif-method	RBPMotif-class
motifLength	RBPMotif-class
motifLength,RBPMotif-method	RBPMotif-class
motifMatrix	RBPMotif-class
motifMatrix,RBPMotif-method	RBPMotif-class
motifRbps	RBPMotif-class
motifRbps,RBPMotif-method	RBPMotif-class
motifs	motifs
motifsMetaInfo	motifsMetaInfo
motifSource	RBPMotif-class
motifSource,RBPMotif-method	RBPMotif-class
motifSpecies	RBPMotif-class
motifSpecies,RBPMotif-method	RBPMotif-class
motifType	RBPMotif-class
motifType,RBPMotif-method	RBPMotif-class
pCombine	pCombine
permTestGeometricMean	permTestGeometricMean
plot,RBPMotif,ANY-method	RBPMotif-class
plot,RBPMotif-method	RBPMotif-class
plot,SpectrumScore,ANY-method	SpectrumScore-class
plot,SpectrumScore-method	SpectrumScore-class
RBPMotif-class	RBPMotif-class
runKmerSPMA	runKmerSPMA
runKmerTSMA	runKmerTSMA
runMatrixSPMA	runMatrixSPMA
runMatrixTSMA	runMatrixTSMA
scoreSequences	scoreSequences
scoreSpectrum	scoreSpectrum
scoreTranscripts	scoreTranscripts
scoreTranscriptsSingleMotif	scoreTranscriptsSingleMotif
setMotifs	setMotifs
show,RBPMotif-method	RBPMotif-class
show,SpectrumScore-method	SpectrumScore-class
spectrumAdjRSquared	SpectrumScore-class
spectrumAdjRSquared,SpectrumScore-method	SpectrumScore-class
spectrumClassifier	spectrumClassifier
spectrumConsistencyScore	SpectrumScore-class
spectrumConsistencyScore,SpectrumScore-method	SpectrumScore-class
spectrumConsistencyScoreN	SpectrumScore-class
spectrumConsistencyScoreN,SpectrumScore-method	SpectrumScore-class
spectrumConsistencyScorePValue	SpectrumScore-class
spectrumConsistencyScorePValue,SpectrumScore-method	SpectrumScore-class
spectrumDegree	SpectrumScore-class
spectrumDegree,SpectrumScore-method	SpectrumScore-class
spectrumFStatistic	SpectrumScore-class
spectrumFStatistic,SpectrumScore-method	SpectrumScore-class
spectrumFStatisticPValue	SpectrumScore-class
spectrumFStatisticPValue,SpectrumScore-method	SpectrumScore-class
spectrumResiduals	SpectrumScore-class
spectrumResiduals,SpectrumScore-method	SpectrumScore-class
SpectrumScore-class	SpectrumScore-class
spectrumSlope	SpectrumScore-class
spectrumSlope,SpectrumScore-method	SpectrumScore-class
subdivideData	subdivideData
toy.motif.matrix	toy.motif.matrix
transite	transite
