PWMEnrich-package	PWMEnrich-package
$,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
.inputParamMotifs	dot-inputParamMotifs
.inputParamSequences	dot-inputParamSequences
.inputPFMfromMatrixOrPWM	dot-inputPFMfromMatrixOrPWM
.normalize.bg.seq	dot-normalize.bg.seq
.normargPfm	dot-normargPfm
.normargPriorParams	dot-normargPriorParams
affinitySequenceSet	affinitySequenceSet
as.data.frame	as.data.frame-MotifEnrichmentReport-method
as.data.frame,MotifEnrichmentReport-method	as.data.frame-MotifEnrichmentReport-method
cloverPvalue1seq	cloverPvalue1seq
cloverScore	cloverScore
colMedians	colMedians
colSds	colSds
concatenateSequences	concatenateSequences
cutoffZscore	cutoffZscore
cutoffZscoreSequenceSet	cutoffZscoreSequenceSet
divideRows	divideRows
DNAStringSetToList	DNAStringSetToList
empiricalPvalue	empiricalPvalue
empiricalPvalueSequenceSet	empiricalPvalueSequenceSet
getBackgroundFrequencies	getBackgroundFrequencies
getPromoters	getPromoters
gevPerSequence	gevPerSequence
groupReport	groupReport-MotifEnrichmentResults-method
groupReport,MotifEnrichmentResults-method	groupReport-MotifEnrichmentResults-method
keepFinite	keepFinite
length,PWM-method	operators-PWM
logNormPval	logNormPval
logNormPvalSequenceSet	logNormPvalSequenceSet
makeBackground	makeBackground
makePriors	makePriors
makePWMCutoffBackground	makePWMCutoffBackground
makePWMEmpiricalBackground	makePWMEmpiricalBackground
makePWMGEVBackground	makePWMGEVBackground
makePWMLognBackground	makePWMLognBackground
makePWMPvalCutoffBackground	makePWMPvalCutoffBackground
makePWMPvalCutoffBackgroundFromSeq	makePWMPvalCutoffBackgroundFromSeq
makeStartEndPos	makeStartEndPos
matrixShuffleZscorePerSequence	matrixShuffleZscorePerSequence
maxAligned	maxAligned
motifDiffEnrichment	motifDiffEnrichment
motifEcdf	motifEcdf
motifEnrichment	motifEnrichment
MotifEnrichmentReport-class	MotifEnrichmentReport-class
MotifEnrichmentResults-class	MotifEnrichmentResults-class
motifIC	motifIC
motifPrAUC	motifPrAUC
motifRankingForGroup	motifRankingForGroup-MotifEnrichmentResults-method
motifRankingForGroup,MotifEnrichmentResults-method	motifRankingForGroup-MotifEnrichmentResults-method
motifRankingForSequence	motifRankingForSequence-MotifEnrichmentResults-method
motifRankingForSequence,MotifEnrichmentResults-method	motifRankingForSequence-MotifEnrichmentResults-method
motifRecoveryAUC	motifRecoveryAUC
motifScores	motifScores
motifScoresBigMemory	motifScoresBigMemory
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,MotifEnrichmentReport,missing-method	plot-MotifEnrichmentReport-missing-method
plot,PWM,missing-method	plot-PWM-missing-method
plotMotifScores	plotMotifScores
plotMultipleMotifs	plotMultipleMotifs
plotPFM	plotPFM
plotTopMotifsGroup	plotTopMotifsGroup-MotifEnrichmentResults-method
plotTopMotifsGroup,MotifEnrichmentResults-method	plotTopMotifsGroup-MotifEnrichmentResults-method
plotTopMotifsSequence	plotTopMotifsSequence-MotifEnrichmentResults-method
plotTopMotifsSequence,MotifEnrichmentResults-method	plotTopMotifsSequence-MotifEnrichmentResults-method
PWM-class	PWM-class
PWMCutoffBackground-class	PWMCutoffBackground-class
PWMEmpiricalBackground-class	PWMEmpiricalBackground-class
PWMEnrich	PWMEnrich-package
PWMGEVBackground-class	PWMGEVBackground-class
PWMLognBackground-class	PWMLognBackground-class
PWMUnscaled	PWMUnscaled
rankingProcessAndReturn	rankingProcessAndReturn
readJASPAR	readJASPAR
readMotifs	readMotifs
readTRANSFAC	readTRANSFAC
registerCoresPWMEnrich	registerCoresPWMEnrich
reverseComplement,PWM-method	reverseComplement-PWM-method
scanWithPWM	scanWithPWM
seqLogoGrid	seqLogoGrid
sequenceReport	sequenceReport-MotifEnrichmentResults-method
sequenceReport,MotifEnrichmentResults-method	sequenceReport-MotifEnrichmentResults-method
show,MotifEnrichmentReport-method	show-MotifEnrichmentReport-method
show,MotifEnrichmentResults-method	show-MotifEnrichmentResults-method
show,PWM-method	show-PWM-method
show,PWMCutoffBackground-method	show-PWMCutoffBackground-method
show,PWMEmpiricalBackground-method	show-PWMEmpiricalBackground-method
show,PWMGEVBackground-method	show-PWMGEVBackground-method
show,PWMLognBackground-method	show-PWMLognBackground-method
toPWM	toPWM
tryAllMotifAlignments	tryAllMotifAlignments
useBigMemoryPWMEnrich	useBigMemoryPWMEnrich
[,MotifEnrichmentReport-method	operators-MotifEnrichmentReport
[,PWMCutoffBackground-method	subsetting-PWMCutoffBackground
[,PWMEmpiricalBackground-method	subsetting-PWMEmpiricalBackground
[,PWMGEVBackground-method	subsetting-PWMGEVBackground
[,PWMLognBackground-method	subsetting-PWMLognBackground
