$,PWM-method	operators-dash-PWM
$,PWMCutoffBackground-method	operators-dash-PWMCutoffBackground
$,PWMEmpiricalBackground-method	operators-dash-PWMEmpiricalBackground
$,PWMGEVBackground-method	operators-dash-PWMGEVBackground
$,PWMLognBackground-method	operators-dash-PWMLognBackground
.inputParamMotifs	dot-inputParamMotifs
.inputParamSequences	dot-inputParamSequences
.inputPFMfromMatrixOrPWM	dot-inputPFMfromMatrixOrPWM
.normalize.bg.seq	dot-normalize-dot-bg-dot-seq
.normargPfm	dot-normargPfm
.normargPriorParams	dot-normargPriorParams
affinitySequenceSet	affinitySequenceSet
cloverPvalue1seq	cloverPvalue1seq
cloverScore	cloverScore
colMedians	colMedians
colSds	colSds
cutoffZscore	cutoffZscore
cutoffZscoreSequenceSet	cutoffZscoreSequenceSet
divideRows	divideRows
DNAStringSetToList	DNAStringSetToList
empiricalPvalue	empiricalPvalue
empiricalPvalueSequenceSet	empiricalPvalueSequenceSet
getBackgroundFrequencies	getBackgroundFrequencies
gevPerSequence	gevPerSequence
keepFinite	keepFinite
length	operators-dash-PWM
length,PWM-method	operators-dash-PWM
logNormPval	logNormPval
logNormPvalSequenceSet	logNormPvalSequenceSet
makeBackground	makeBackground
makePriors	makePriors
makePWMCutoffBackground	makePWMCutoffBackground
makePWMEmpiricalBackground	makePWMEmpiricalBackground
makePWMGEVBackground	makePWMGEVBackground
makePWMLognBackground	makePWMLognBackground
makePWMPvalCutoffBackground	makePWMPvalCutoffBackground
makeStartEndPos	makeStartEndPos
matrixShuffleZscorePerSequence	matrixShuffleZscorePerSequence
maxAligned	maxAligned
motifDiffEnrichment	motifDiffEnrichment
motifEnrichment	motifEnrichment
motifIC	motifIC
motifScores	motifScores
motifSimilarity	motifSimilarity
names,PWM-method	operators-dash-PWM
names,PWMCutoffBackground-method	operators-dash-PWMCutoffBackground
names,PWMEmpiricalBackground-method	operators-dash-PWMEmpiricalBackground
names,PWMGEVBackground-method	operators-dash-PWMGEVBackground
names,PWMLognBackground-method	operators-dash-PWMLognBackground
PFMtoPWM	PFMtoPWM
plot	plot-comma-PWM-comma-missing-dash-method
plot,PWM,missing-method	plot-comma-PWM-comma-missing-dash-method
plotMultipleMotifs	plotMultipleMotifs
plotPFM	plotPFM
PWM	PWM-dash-class
PWM-class	PWM-dash-class
PWMCutoffBackground	PWMCutoffBackground-dash-class
PWMCutoffBackground-class	PWMCutoffBackground-dash-class
PWMEmpiricalBackground	PWMEmpiricalBackground-dash-class
PWMEmpiricalBackground-class	PWMEmpiricalBackground-dash-class
PWMGEVBackground	PWMGEVBackground-dash-class
PWMGEVBackground-class	PWMGEVBackground-dash-class
PWMLognBackground	PWMLognBackground-dash-class
PWMLognBackground-class	PWMLognBackground-dash-class
PWMUnscaled	PWMUnscaled
readJASPAR	readJASPAR
readMotifs	readMotifs
readTRANSFAC	readTRANSFAC
registerCoresPWMEnrich	registerCoresPWMEnrich
reverseComplement	reverseComplement-comma-PWM-dash-method
reverseComplement,PWM-method	reverseComplement-comma-PWM-dash-method
scanWithPWM	scanWithPWM
seqLogoGrid	seqLogoGrid
show,PWM-method	show-comma-PWM-dash-method
show,PWMCutoffBackground-method	show-comma-PWMCutoffBackground-dash-method
show,PWMEmpiricalBackground-method	show-comma-PWMEmpiricalBackground-dash-method
show,PWMGEVBackground-method	show-comma-PWMGEVBackground-dash-method
show,PWMLognBackground-method	show-comma-PWMLognBackground-dash-method
tryAllMotifAlignments	tryAllMotifAlignments
