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.
Modstrings-internals    Modstrings internals
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 modification
                        information into/from a 'XString' and a
                        'GRanges' object
shortName               Base information for sequence characters of
                        nucleotide strings containing modifications
