&,filters,filters-method	filter-methods
alignments-class	aligns-class
combine	combine
combine,motiv,filters-method	combine
combine,motiv,list-method	combine
combine-method	combine
cooccurences	motifOccurences
exportAsRangedData	exportAsRangedData
exportAsTransfacFile	exportAsTransfacFile
filter	filter
filter,motiv,filters-method	filter
filter,motiv,list-method	filter
filter-class	filter-class
filter-methods	filter
generateDBScores	generateDBScores
getGademPWM	getGademPWM
jaspar	jaspar
jaspar.scores	jaspar
length,motiv-method	motiv-methods
makePWM	makePWM
matches-class	matches-class
motifMatch	motifMatch
motiv	motiv-methods
motiv-class	motiv-class
names,motiv-method	motiv-methods
names<-,motiv-method	motiv-methods
occurences	motifOccurences
plot,motiv,ANY-method	plot
plot,motiv,gadem-method	plot
plot,motiv-method	plot
plot-methods	plot
readDBScores	generateDBScores
readGademPWMFile	readGademPWMFile
readPWMfile	readPWMfile
seqLogo	seqLogo
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-method	motiv-methods
|,filters,filters-method	filter-methods
