alphabetFrequency       XNAAlphabetFrequency returns letters frequency
                        for a given object in base, sugar or backbone
                        slot
backbone                Backbone setter/getter method
base                    Base setter/getter method
changeBase              Translate base slot based on complementary
                        bases dictionary. Base sequence in transformed
                        using compl_target column.
compl_dictionary        Compl_dictionary setter/getter method
complementary_bases     Default XNAString complementarity dictionary
concatDict              Concatenate HELM-symbol custom dictionary with
                        built-in HELM-symbol dictionary
                        (xna_dictionary)
conjugate3              Conjugate3 setter/getter method
conjugate5              Conjugate5 setter/getter method
default_backbone        Default_backbone setter/getter method
default_sugar           Default_sugar setter/getter method
dictionary              Dictionary setter/getter method
dinucleotideFrequency   XNADinucleotideFrequencyFun returns double
                        letters frequency for a given object in base,
                        sugar or backbone slot
dt2Set                  Function which creates XNAstringSet object from
                        table with base, sugar and backbone columns.
duplex_structure        Duplex_structure setter/getter method
helm2String             Translate RNA from HELM notation to
                        multi-string notation
instanceOf              Check on an object type
listOflists2Dt          Save list of lists as data.table
mimir2XnaDict           Reformat mimir table to XNA dictionary
                        standards
name                    Name setter/getter method
objects                 Objects getter method for XNAStringSet class
parseRnaHelmComponent   Parse monomers from HELM to multi-string
                        notation
predictDuplexStructure
                        Compute Minimum Free Energy (MFE), and a
                        corresponding secondary structure for two
                        dimerized RNA sequences.
predictMfeStructure     Prediction of MFE structure with ViennaRNA
                        package
reverseComplementFun    Reverse complement sequence based on dictionary
secondary_structure     Secondary_structure setter/getter method
seqAlphabetFrequency    Create set of functions and methods to
                        calculate alphabet frequency in base, sugar and
                        backbone slots
seqDinucleotideFrequency
                        Create set of functions and methods to
                        calculate dinucleotide frequency in base, sugar
                        and backbone slots
seqVectorAlphabetFrequency
                        seqVectorAlphabetFrequency function calculates
                        frequency for strings vector
seqVectorDinucleotideFrequency
                        seqVectorDinucleotideFrequency function
                        calculates frequency for strings vector
set2Dt                  set2Dt function - changes XNAStringSet object
                        to data.table
set2List                Define method to save XNAStringSet object as a
                        list of XNAString objects
siRNA_HELM              siRNA_HELM function takes XNAString object and
                        returns pairing information for base slot.
                        Works only for double stranded molecules.
sugar                   Sugar setter/getter method
target                  Target setter/getter method
typedListCheck          Check if all objects are of XNAString class and
                        dictionaries are the same
uniqueChars             Utility functions useful when programming and
                        developing XNAString class
xna_dictionary          Default XNAString dictionary
XNAMatchPattern         Finds pattern in reference sequence
XNAMatchPDict           Find set of patterns in reference sequence
xnaObj2Dt               xnaObj2Dt function - changes XNAString object
                        to data.table
XNAPairwiseAlignment    Pairwise alignment methods for XNAString object
XNAReverseComplement    Reverse complement sequence based on dictionary
XNAString-class         Development of XNAString class aims at enabling
                        efficient manipulation of modified
                        oligonucleotide sequences. The class consists
                        of the following slots: name, base, sugar,
                        backbone, target, conjugate5, conjugate3,
                        secondary_structure, duplex_structure,
                        dictionary (HELM-string dictionary),
                        compl_dictionary.
XNAString2XNAStringSet
                        XNAString2XNAStringSet function - changes
                        XNAString object to XNAStringSet
xnastringClassUnions    setClassUnion definitions
xnastringElementsNumber
                        Function which checks if XNAString object
                        satisfies predefined slots length
XNAStringFromHelm       Create XNAString object from HELM - user
                        interface
XNAStringSet-class      Create class which consists of XNAString
                        objects given as a list
XNAStringToHelm         XNAStringToHelmFun function takes XNAString
                        object and translates base, sugar and backbone
                        to HELM notation
XNAVmatchPattern        This is function finding all the occurrences of
                        a given pattern (typically short) in a
                        (typically long) set of reference sequences.
