&,filters,filters-method	filter-methods
alignments-class	aligns-class
as.data.frame	as.data.frame
as.data.frame,motiv-method	as.data.frame
as.data.frame-methods	as.data.frame
combineMotifs	combineMotifs
combineMotifs,motiv,filters-method	combineMotifs
combineMotifs,motiv,list-method	combineMotifs
combineMotifs-method	combineMotifs
cooccurences	motifOccurences
exportAsRangedData	exportAsRangedData
exportAsTransfacFile	exportAsTransfacFile
exportAsTransfacFile,list-method	exportAsTransfacFile
exportAsTransfacFile,motiv-method	exportAsTransfacFile
exportAsTransfacFile-methods	exportAsTransfacFile
filter	filter
filter,motiv,filters-method	filter
filter,motiv,list-method	filter
filter-class	filter-class
filter-methods	filter
FOXA	FOXA_rGADEM
FOXA1_rGADEM	FOXA_rGADEM
gadem	FOXA_rGADEM
generateDBScores	generateDBScores
getGademPWM	getGademPWM
getPWM	getPWM
getPWM,motiv-method	getPWM
getPWM-methods	getPWM
jaspar	jaspar
jaspar.scores	jaspar
length,motiv-method	motiv-methods
makePWM	makePWM
matches-class	matches-class
motifCutree	motifDistance
motifDistances	motifDistance
motifHclust	motifDistance
motifMatch	motifMatch
motiv	motiv-methods
motiv-class	motiv-class
names,filter-method	filter-methods
names,filters-method	filter-methods
names,motiv-method	motiv-methods
names<-,motiv-method	motiv-methods
occurences	motifOccurences
plot	plot
plot,motiv,ANY-method	plot
plot,motiv,gadem-method	plot
plot,motiv-method	plot
plot-methods	plot
readDBScores	generateDBScores
readGademPWMFile	readGademPWMFile
readPWMfile	readPWMfile
seqLogo2	seqLogo2
setFilter	setFilter
show,filter-method	filter-methods
show,motiv-method	motiv-methods
similarity	motiv-methods
similarity,list-method	motiv-methods
similarity,motiv-method	motiv-methods
split,motiv,filters-method	split
split,motiv,list-method	split
split-methods	split
summary,filter-method	filter-methods
summary,filters-method	filter-methods
summary,list-method	motiv-methods
summary,motiv-method	motiv-methods
transcriptionFactor-class	tf-class
trimPWMedge	trimPWMedge
viewAlignments	viewAlignment
viewMotifs	viewMotifs
viewMotifs,motiv-method	viewMotifs
viewMotifs-methods	viewMotifs
writeDBScores	generateDBScores
[,motiv,ANY,ANY-method	motiv-methods
[,motiv-method	motiv-methods
|,filters,filters-method	filter-methods
