alignPwmSets	alignPwmSets
Alphabet	Alphabet
ASN	ASN
baseDistributionPwm	baseDistributionPwm
calculatePvalue	calculatePvalue
createDiffLogoObject	createDiffLogoObject
differenceOfICs	differenceOfICs
diffLogo	diffLogo
diffLogoFromPwm	diffLogoFromPwm
diffLogoTable	diffLogoTable
diffLogoTableConfiguration	diffLogoTableConfiguration
DNA	DNA
drawDiffLogoTable	drawDiffLogoTable
enrichDiffLogoObjectWithPvalues	enrichDiffLogoObjectWithPvalues
enrichDiffLogoTableWithPvalues	enrichDiffLogoTableWithPvalues
extendPwmsFromAlignmentVector	extendPwmsFromAlignmentVector
FULL_ALPHABET	FULL_ALPHABET
getAlphabetFromCharacters	getAlphabetFromCharacters
getAlphabetFromSequences	getAlphabetFromSequences
getPwmFromAlignment	getPwmFromAlignment
getPwmFromAlignmentFile	getPwmFromAlignmentFile
getPwmFromFastaFile	getPwmFromFastaFile
getPwmFromFile	getPwmFromFile
getPwmFromHomerFile	getPwmFromHomerFile
getPwmFromPfmOrJasparFile	getPwmFromPfmOrJasparFile
getPwmFromPwmFile	getPwmFromPwmFile
getSequencesFromAlignmentFile	getSequencesFromAlignmentFile
getSequencesFromFastaFile	getSequencesFromFastaFile
informationContent	informationContent
localPwmAlignment	localPwmAlignment
lossOfAbsICDifferences	lossOfAbsICDifferences
multipleLocalPwmsAlignment	multipleLocalPwmsAlignment
normalizedDifferenceOfProbabilities	normalizedDifferenceOfProbabilities
normalizePWM	normalizePWM
prepareDiffLogoTable	prepareDiffLogoTable
probabilities	probabilities
pwmDivergence	pwmDivergence
pwmsDistanceMatrix	pwmsDistanceMatrix
reverseAlignmentVector	reverseAlignmentVector
RNA	RNA
seqLogo	seqLogo
shannonDivergence	shannonDivergence
sumOfAbsICDifferences	sumOfAbsICDifferences
sumOfAbsProbabilityDifferences	sumOfAbsProbabilityDifferences
sumProbabilities	sumProbabilities
switchDirection	switchDirection
twoSetsAveragePwmDivergenceFromAlignmentVector	twoSetsAveragePwmDivergenceFromAlignmentVector
