$,MotifEnrichmentReport-method	operators-MotifEnrichmentReport
$,MotifEnrichmentResults-method	operators-MotifEnrichmentResults
$,PWM-method	operators-PWM
$,PWMCutoffBackground-method	operators-PWMCutoffBackground
$,PWMEmpiricalBackground-method	operators-PWMEmpiricalBackground
$,PWMGEVBackground-method	operators-PWMGEVBackground
$,PWMLognBackground-method	operators-PWMLognBackground
as.data.frame	as.data.frame-commaMotifEnrichmentReport-method
as.data.frame,MotifEnrichmentReport-method	as.data.frame-commaMotifEnrichmentReport-method
getBackgroundFrequencies	getBackgroundFrequencies
groupReport	groupReport-commaMotifEnrichmentResults-method
groupReport,MotifEnrichmentResults-method	groupReport-commaMotifEnrichmentResults-method
length	operators-PWM
length,PWM-method	operators-PWM
makeBackground	makeBackground
makePriors	makePriors
makePWMCutoffBackground	makePWMCutoffBackground
makePWMEmpiricalBackground	makePWMEmpiricalBackground
makePWMGEVBackground	makePWMGEVBackground
makePWMLognBackground	makePWMLognBackground
makePWMPvalCutoffBackground	makePWMPvalCutoffBackground
makePWMPvalCutoffBackgroundFromSeq	makePWMPvalCutoffBackgroundFromSeq
motifDiffEnrichment	motifDiffEnrichment
motifEcdf	motifEcdf
motifEnrichment	motifEnrichment
MotifEnrichmentReport	MotifEnrichmentReport
MotifEnrichmentReport-class	MotifEnrichmentReport
MotifEnrichmentResults	MotifEnrichmentResults
MotifEnrichmentResults-class	MotifEnrichmentResults
motifIC	motifIC
motifRankingForGroup	motifRankingForGroup-commaMotifEnrichmentResults-method
motifRankingForGroup,MotifEnrichmentResults-method	motifRankingForGroup-commaMotifEnrichmentResults-method
motifRankingForSequence	motifRankingForSequence-commaMotifEnrichmentResults-method
motifRankingForSequence,MotifEnrichmentResults-method	motifRankingForSequence-commaMotifEnrichmentResults-method
motifScores	motifScores
motifSimilarity	motifSimilarity
names,MotifEnrichmentReport	operators-MotifEnrichmentReport
names,MotifEnrichmentReport-method	operators-MotifEnrichmentReport
names,MotifEnrichmentResults	operators-MotifEnrichmentResults
names,MotifEnrichmentResults-method	operators-MotifEnrichmentResults
names,PWM	operators-PWM
names,PWM-method	operators-PWM
names,PWMCutoffBackground	operators-PWMCutoffBackground
names,PWMCutoffBackground-method	operators-PWMCutoffBackground
names,PWMEmpiricalBackground	operators-PWMEmpiricalBackground
names,PWMEmpiricalBackground-method	operators-PWMEmpiricalBackground
names,PWMGEVBackground	operators-PWMGEVBackground
names,PWMGEVBackground-method	operators-PWMGEVBackground
names,PWMLognBackground	operators-PWMLognBackground
names,PWMLognBackground-method	operators-PWMLognBackground
PFMtoPWM	PFMtoPWM
plot	plot
plot,MotifEnrichmentReport,missing-method	plot
plot,PWM,missing-method	plot
plotMotifScores	plotMotifScores
plotMultipleMotifs	plotMultipleMotifs
plotTopMotifsGroup	plotTopMotifsGroup-commaMotifEnrichmentResults-method
plotTopMotifsGroup,MotifEnrichmentResults-method	plotTopMotifsGroup-commaMotifEnrichmentResults-method
plotTopMotifsSequence	plotTopMotifsSequence-commaMotifEnrichmentResults-method
plotTopMotifsSequence,MotifEnrichmentResults-method	plotTopMotifsSequence-commaMotifEnrichmentResults-method
PWM	PWM
PWM-class	PWM
PWMCutoffBackground	PWMCutoffBackground
PWMCutoffBackground-class	PWMCutoffBackground
PWMEmpiricalBackground	PWMEmpiricalBackground
PWMEmpiricalBackground-class	PWMEmpiricalBackground
PWMGEVBackground	PWMGEVBackground
PWMGEVBackground-class	PWMGEVBackground
PWMLognBackground	PWMLognBackground
PWMLognBackground-class	PWMLognBackground
PWMUnscaled	PWMUnscaled
readMotifs	readMotifs
registerCoresPWMEnrich	registerCoresPWMEnrich
reverseComplement	reverseComplement
reverseComplement,PWM-method	reverseComplement
scanWithPWM	scanWithPWM
seqLogoGrid	seqLogoGrid
sequenceReport	sequenceReport-commaMotifEnrichmentResults-method
sequenceReport,MotifEnrichmentResults-method	sequenceReport-commaMotifEnrichmentResults-method
toPWM	toPWM
useBigMemoryPWMEnrich	useBigMemoryPWMEnrich
[,MotifEnrichmentReport-method	operators-MotifEnrichmentReport
[,PWMCutoffBackground-method	subsetting-PWMCutoffBackground
[,PWMEmpiricalBackground-method	subsetting-PWMEmpiricalBackground
[,PWMGEVBackground-method	subsetting-PWMGEVBackground
[,PWMLognBackground-method	subsetting-PWMLognBackground
