MaskedModString         MaskedModString objects
ModDNAString            ModDNAString class
ModRNAString            ModDNAString class
ModString               ModString objects
ModStringSet            ModStringSet objects
ModStringSet-io         Read/write an ModStringSet object from/to a
                        file
ModStringSetList        ModStringSetList
ModStringViews          The ModStringViews class extending the
                        XStringViews class
Modstrings              Modstrings: implementation of Biostrings to
                        work with nucleotide sequences containing
                        modified nucleotides.
QualityScaledModStringSet
                        QualityScaledModDNAStringSet and
                        QualityScaledModRNAStringSet objects
letterFrequency         Calculate the frequency of letters in
                        nucleotide sequence with modifications, or the
                        consensus matrix of a set of sequences
modifyNucleotides       Modifying nucleotides in a nucleotide sequence
                        (or set of sequences) at specified locations
replaceLetterAt         Replacing letters in a nucleotide sequence (or
                        set of nucleotide sequences) at some specified
                        locations containing nucleotide modifications
sanitizeInput           Sanitize input strings for use with ModString
                        classes
separate                Separating and combining a ModString object
                        into/from a XString and a GRanges object
shortName               Base information for sequence characters of
                        nucleotide strings containing modifications
