motifStack-package	motifStack-package
$,marker-method	marker-class
$,motifSig-method	motifSig-class
$,ouNode-method	ouNode-class
$,pcm-method	pcm-class
$,pfm-method	pfm-class
$,psam-method	psam-class
$,pssm-method	pssm-class
$<-,marker-method	marker-class
$<-,motifSig-method	motifSig-class
$<-,ouNode-method	ouNode-class
$<-,pcm-method	pcm-class
$<-,pfm-method	pfm-class
$<-,psam-method	psam-class
$<-,pssm-method	pssm-class
AAmotifAlignment	AAmotifAlignment
addBlank	pcm-class
addBlank,pcm,numeric,logical-method	pcm-class
addBlank,pfm,numeric,logical-method	pfm-class
addBlank,psam,numeric,logical-method	psam-class
addBlank,pssm,numeric,logical-method	pssm-class
as	pcm-class
as()	psam-class
as.data.frame,pcm-method	pcm-class
as.data.frame,pfm-method	pfm-class
as.data.frame,psam-method	psam-class
as.data.frame,pssm-method	pssm-class
browseMotifs	browseMotifs
browseMotifs-shiny	browseMotifs-shiny
browseMotifsOutput	browseMotifs-shiny
calF	calF
calI	calI
clusterMotifs	clusterMotifs
coerce	pfm-class
coerce()	pssm-class
coerce,pcm,matrix-method	pcm-class
coerce,pfm,matrix-method	pfm-class
coerce,psam,matrix-method	psam-class
coerce,pssm,matrix-method	pssm-class
colorset	colorset
compare2profiles	compare2profiles
compareProfiles	compareProfiles
DNAmotifAlignment	DNAmotifAlignment
DNAmotifToRNAmotif	DNAmotifToRNAmotif
dpGlobal	dpGlobal
dpLocal	dpLocal
format,pcm-method	pcm-class
format,pfm-method	pfm-class
format,psam-method	psam-class
format,pssm-method	pssm-class
frequence	motifSig-class
frequence,motifSig-method	motifSig-class
GeomMotif	GeomMotif
geom_motif	geom_motif
getALLRscoreFromCounts	getALLRscoreFromCounts
getDistance	getDistance
getIC	pcm-class
getIC,matrix,matrix-method	pfm-class
getIC,matrix,numeric-method	pfm-class
getIC,pcm,ANY-method	pcm-class
getIC,pfm,ANY-method	pfm-class
getRankedUniqueMotifs	getRankedUniqueMotifs
getScore	getScore
highlightCol	highlightCol
importMatrix	importMatrix
marker	marker-class
marker-class	marker-class
matalign	matalign
matrixReverseComplement	pcm-class
matrixReverseComplement,pcm-method	pcm-class
matrixReverseComplement,pfm-method	pfm-class
matrixReverseComplement,psam-method	psam-class
matrixReverseComplement,pssm-method	pssm-class
mergeMotifs	mergeMotifs
motifCircos	motifCircos
motifCloud	motifCloud
motifGrob	motifGrob
motifHclust	motifHclust
motifPiles	motifPiles
motifSig	motifSig-class
motifSig-class	motifSig-class
motifSignature	motifSignature
motifStack	motifStack
nodelist	motifSig-class
nodelist,motifSig-method	motifSig-class
ouNode	ouNode-class
ouNode-class	ouNode-class
pcm	pcm-class
pcm-class	pcm-class
pcm2pfm	pcm-class
pcm2pfm,data.frame,ANY-method	pcm-class
pcm2pfm,data.frame,numeric-method	pcm-class
pcm2pfm,list,ANY-method	pcm-class
pcm2pfm,list,numeric-method	pcm-class
pcm2pfm,matrix,ANY-method	pcm-class
pcm2pfm,matrix,numeric-method	pcm-class
pcm2pfm,pcm,ANY-method	pcm-class
pcm2pssm	pcm-class
pcm2pssm,data.frame,ANY-method	pcm-class
pcm2pssm,data.frame,numeric-method	pcm-class
pcm2pssm,list,ANY-method	pcm-class
pcm2pssm,list,numeric-method	pcm-class
pcm2pssm,matrix,ANY-method	pcm-class
pcm2pssm,matrix,numeric-method	pcm-class
pcm2pssm,pcm,ANY-method	pcm-class
pfm	pfm-class
pfm-class	pfm-class
pfm2pwm	pfm2pwm
plot	pcm-class
plot,pcm,ANY-method	pcm-class
plot,pfm,ANY-method	pfm-class
plot,psam,ANY-method	psam-class
plot,pssm,ANY-method	pssm-class
plotAffinityLogo	plotAffinityLogo
plotMotifLogo	plotMotifLogo
plotMotifLogoA	plotMotifLogoA
plotMotifLogoStack	plotMotifLogoStack
plotMotifLogoStackWithTree	plotMotifLogoStackWithTree
plotMotifOverMotif	plotMotifOverMotif
plotMotifStackWithPhylog	plotMotifStackWithPhylog
plotMotifStackWithRadialPhylog	plotMotifStackWithRadialPhylog
plotXaxis	plotXaxis
plotYaxis	plotYaxis
psam	psam-class
psam-class	psam-class
pssm	pssm-class
pssm-class	pssm-class
readPCM	readPCM
renderbrowseMotifs	browseMotifs-shiny
reorderUPGMAtree	reorderUPGMAtree
sigColor	motifSig-class
sigColor,motifSig-method	motifSig-class
signatures	motifSig-class
signatures,motifSig-method	motifSig-class
traceBackGlobal	traceBackGlobal
traceBackLocal	traceBackLocal
trimMotif	pcm-class
trimMotif,pcm,numeric-method	pcm-class
trimMotif,pfm,numeric-method	pfm-class
_PACKAGE	motifStack-package
