# Generated by roxygen2: do not edit by hand

export(ASN)
export(Alphabet)
export(DNA)
export(FULL_ALPHABET)
export(RNA)
export(calculatePvalue)
export(createDiffLogoObject)
export(diffLogo)
export(diffLogoFromPwm)
export(diffLogoTable)
export(diffLogoTableConfiguration)
export(differenceOfICs)
export(drawDiffLogoTable)
export(enrichDiffLogoObjectWithPvalues)
export(enrichDiffLogoTableWithPvalues)
export(extendPwmsFromAlignmentVector)
export(getAlphabetFromCharacters)
export(getAlphabetFromSequences)
export(getPwmFromAlignment)
export(getPwmFromAlignmentFile)
export(getPwmFromFastaFile)
export(getPwmFromFile)
export(getPwmFromHomerFile)
export(getPwmFromPfmOrJasparFile)
export(getPwmFromPwmFile)
export(getSequencesFromAlignmentFile)
export(getSequencesFromFastaFile)
export(informationContent)
export(lossOfAbsICDifferences)
export(multipleLocalPwmsAlignment)
export(normalizePWM)
export(normalizedDifferenceOfProbabilities)
export(prepareDiffLogoTable)
export(probabilities)
export(pwmDivergence)
export(seqLogo)
export(shannonDivergence)
export(sumOfAbsICDifferences)
export(sumOfAbsProbabilityDifferences)
export(sumProbabilities)
exportClasses(Alphabet)
exportClasses(DiffLogo)
importFrom("cba", "order.optimal")
importFrom("grDevices", "colorRampPalette", "rgb")
importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "plot.new", "polygon", "rect", "text")
importFrom("stats", "dgamma", "dist", "hclust", "var")
importFrom("utils", "modifyList", "read.delim")
importFrom("tools", "file_ext")
