motifStack-package	motifStack-package
$,motifSig-method	motifSig-methods
$,ouNode-method	ouNode-class
$,pcm-method	pcm-methods
$,pfm-method	pfm-methods
$<-,motifSig-method	motifSig-methods
$<-,ouNode-method	ouNode-class
$<-,pcm-method	pcm-methods
$<-,pfm-method	pfm-methods
addBlank	pfm-methods
addBlank,pcm,numeric,logical-method	pcm-methods
addBlank,pfm,numeric,logical-method	pfm-methods
colorset	colorset
DNAmotifAlignment	DNAmotifAlignment
frequence	motifSig-methods
frequence,motifSig-method	motifSig-methods
getIC	pfm-methods
getIC,matrix,matrix-method	pfm-methods
getIC,matrix,numeric-method	pfm-methods
getIC,pcm,ANY-method	pcm-methods
getIC,pfm,ANY-method	pfm-methods
getRankedUniqueMotifs	getRankedUniqueMotifs
highlightCol	highlightCol
matrixReverseComplement	pfm-methods
matrixReverseComplement,pcm-method	pcm-methods
matrixReverseComplement,pfm-method	pfm-methods
mergeMotifs	mergeMotifs
motifCircos	motifCircos
motifCloud	motifCloud
motifPiles	motifPiles
motifSig	motifSig-methods
motifSig-class	motifSig-class
motifSignature	motifSignature
motifStack	motifStack
nodelist	motifSig-methods
nodelist,motifSig-method	motifSig-methods
ouNode	ouNode-class
ouNode-class	ouNode-class
pcm	pcm-methods
pcm-class	pcm-class
pcm2pfm	pcm-methods
pcm2pfm,data.frame,ANY-method	pcm-methods
pcm2pfm,data.frame,numeric-method	pcm-methods
pcm2pfm,matrix,ANY-method	pcm-methods
pcm2pfm,matrix,numeric-method	pcm-methods
pcm2pfm,pcm,ANY-method	pcm-methods
pfm	pfm-methods
pfm-class	pfm-class
pfm2pwm	pfm2pwm
plot,pcm,ANY-method	pcm-methods
plot,pfm,ANY-method	pfm-methods
plotMotifLogo	plotMotifLogo
plotMotifLogoA	plotMotifLogoA
plotMotifLogoStack	plotMotifLogoStack
plotMotifLogoStackWithTree	plotMotifLogoStackWithTree
plotMotifOverMotif	plotMotifOverMotif
plotMotifStackWithPhylog	plotMotifStackWithPhylog
plotMotifStackWithRadialPhylog	plotMotifStackWithRadialPhylog
plotXaxis	plotXaxis
plotYaxis	plotYaxis
readPCM	readPCM
reorderUPGMAtree	reorderUPGMAtree
sigColor	motifSig-methods
sigColor,motifSig-method	motifSig-methods
signatures	motifSig-methods
signatures,motifSig-method	motifSig-methods
trimMotif	pcm-methods
trimMotif,pcm,numeric-method	pcm-methods
trimMotif,pfm,numeric-method	pfm-methods
