ASN                     ASN alphabet
Alphabet                built alphabet
DNA                     DNA alphabet
FULL_ALPHABET           Complete character alphabet
RNA                     RNA alphabet
alignPwmSets            Multiple PWMs alignment
baseDistributionPwm     Generates a PWM
calculatePvalue         p-value that two PWM-positions are from the
                        same distribution
createDiffLogoObject    DiffLogo object
diffLogo                Draw DiffLogo
diffLogoFromPwm         Draw DiffLogo from PWM
diffLogoTable           Draw DiffLogo-table
diffLogoTableConfiguration
                        Configuration object for diffLogoTable
differenceOfICs         normalized information content differences
drawDiffLogoTable       Draws a table of DiffLogos
enrichDiffLogoObjectWithPvalues
                        Enriches a difflogo object with p-values
enrichDiffLogoTableWithPvalues
                        Enriches a matrix of difflogo objects with
                        p-values
extendPwmsFromAlignmentVector
                        Extend pwms with respect to alignment
getAlphabetFromCharacters
                        returns the alphabet which fits to the given
                        characters
getAlphabetFromSequences
                        returns the alphabet which fits to the given
                        sequences
getPwmFromAlignment     Create PWM from alignment
getPwmFromAlignmentFile
                        generates a pwm from an alignment file
getPwmFromFastaFile     generates a pwm from a FASTA file
getPwmFromFile          generates a pwm from a file of different
                        formats
getPwmFromHomerFile     generates a pwm from a homer file
getPwmFromPfmOrJasparFile
                        generates a pwm from a jaspar file
getPwmFromPwmFile       generates a pwm from a pwm file
getSequencesFromAlignmentFile
                        extracts the sequences from an alignment file
getSequencesFromFastaFile
                        extracts the sequences from a FASTA file
informationContent      information content
localPwmAlignment       Align pwms
lossOfAbsICDifferences
                        the change of information content
multipleLocalPwmsAlignment
                        Multiple PWMs alignment
normalizePWM            normalizes the given pwm
normalizedDifferenceOfProbabilities
                        normalized probability differences
prepareDiffLogoTable    Prepare a table of difflogo objects
probabilities           probabilities
pwmDivergence           PWM divergence
pwmsDistanceMatrix      Multiple PWMs alignment
reverseAlignmentVector
                        Reverse for alignment vector
seqLogo                 Draw sequence logo
shannonDivergence       shannon divergence
sumOfAbsICDifferences   sum of absolute information content differences
sumOfAbsProbabilityDifferences
                        sum of absolute probability differences
sumProbabilities        sum of probabilities, i.e. 1.0
switchDirection         Switches between 'forward' and 'reverse'
twoSetsAveragePwmDivergenceFromAlignmentVector
                        Average divergence between two sets.
