Bed2Granges	Bed2Granges
combine2Table	combine2Table
combineMotifFiles	combineMotifFiles
combineTestResults	combineTestResults
compareBedFiless2UserProvidedRegions	compareBedFiless2UserProvidedRegions
CompareBeds2GivenRegions	CompareBeds2GivenRegions
CompareMotifs2GivenRegions	CompareMotifs2GivenRegions
compareMotifs2UserProvidedRegions	compareMotifs2UserProvidedRegions
computeFoldEnrichment	computeFoldEnrichment
data	data
decomposeBindingSignal	decomposeBindingSignal
DeleteMultipleFiles	DeleteMultipleFiles
deriveHeuristicBindingDistribution	deriveHeuristicBindingDistribution
DetectBindingSites	DetectBindingSites
DetectBindingSitesBed	DetectBindingSitesBed
DetectBindingSitesMotif	DetectBindingSitesMotif
DetectFdrCutoffBH	DetectFdrCutoffBH
findMotifs	findMotifs
fitKernelDensity	fitKernelDensity
generate1ntBedAlignment	generate1ntBedAlignment
Motif2Site	Motif2Site
motifBindingNegativeBinomialCount	motifBindingNegativeBinomialCount
motifChipCount	motifChipCount
motifCount	motifCount
motifTablePreProcess	motifTablePreProcess
NegativeBinomialTestWithReplicate	NegativeBinomialTestWithReplicate
pairwisDifferential	pairwisDifferential
quiet	quiet
recenterBindingSitesAcrossExperiments	recenterBindingSitesAcrossExperiments
removeNonBellShapedMotifs	removeNonBellShapedMotifs
strongestMotif	strongestMotif
