==,ModString,ModString-method	ModString
==,ModString,XString-method	ModString
==,ModStringSet,ModStringSet-method	ModStringSet
==,ModStringSet,XStringSet-method	ModStringSet
==,ModStringViews,ModStringViews-method	ModStringViews
==,ModStringViews,XString-method	ModStringViews
==,XString,ModString-method	ModString
==,XStringSet,ModStringSet-method	ModStringSet
==,XStringViews,ModString-method	ModStringViews
alphabet	alphabet
alphabet,ModString-method	alphabet
alphabet,ModStringSet-method	alphabet
alphabetFrequency	letterFrequency
alphabetFrequency,MaskedModString-method	letterFrequency
alphabetFrequency,ModDNAString-method	letterFrequency
alphabetFrequency,ModDNAStringSet-method	letterFrequency
alphabetFrequency,ModRNAString-method	letterFrequency
alphabetFrequency,ModRNAStringSet-method	letterFrequency
as.character,ModString-method	ModString
as.character,ModStringSet-method	ModStringSet
as.vector,ModString-method	ModString
combineIntoModstrings	separate
combineIntoModstrings,XString,GRanges-method	separate
combineIntoModstrings,XStringSet,GRanges-method	separate
combineIntoModstrings,XStringSet,GRangesList-method	separate
combineModifications	separate
combineModifications,GRanges-method	separate
combineModifications,GRangesList-method	separate
consensusMatrix,ModStringSet-method	letterFrequency
consensusString	letterFrequency
consensusString,ModDNAStringSet-method	letterFrequency
consensusString,ModRNAStringSet-method	letterFrequency
consensusString,ModStringViews-method	letterFrequency
fullName	alphabet
fullName,ModString-method	alphabet
fullName,ModStringSet-method	alphabet
hasOnlyBaseLetters	letterFrequency
hasOnlyBaseLetters,ModDNAString-method	letterFrequency
hasOnlyBaseLetters,ModDNAStringSet-method	letterFrequency
hasOnlyBaseLetters,ModRNAString-method	letterFrequency
hasOnlyBaseLetters,ModRNAStringSet-method	letterFrequency
incompatibleModifications	separate
incompatibleModifications,GRanges,XString-method	separate
incompatibleModifications,GRanges,XStringSet-method	separate
incompatibleModifications,GRangesList,XStringSet-method	separate
letterFrequency	letterFrequency
letterFrequency,MaskedModString-method	letterFrequency
letterFrequency,ModStringViews-method	letterFrequency
letterFrequencyInSlidingView	letterFrequency
MaskedModString	MaskedModString
ModDNAString	ModDNAString
ModDNAString-class	ModString
ModDNAStringSet	ModStringSet
ModDNAStringSet-class	ModStringSet
ModDNAStringSetList	ModStringSetList
ModDNAStringSetList-class	ModStringSetList
modifyNucleotides	modifyNucleotides
modifyNucleotides,DNAString-method	modifyNucleotides
modifyNucleotides,DNAStringSet-method	modifyNucleotides
modifyNucleotides,ModString-method	modifyNucleotides
modifyNucleotides,ModStringSet-method	modifyNucleotides
modifyNucleotides,RNAString-method	modifyNucleotides
modifyNucleotides,RNAStringSet-method	modifyNucleotides
ModRNAString	ModRNAString
ModRNAString-class	ModString
ModRNAStringSet	ModStringSet
ModRNAStringSet-class	ModStringSet
ModRNAStringSetList	ModStringSetList
ModRNAStringSetList-class	ModStringSetList
modsDNA	Modstrings-internals
modsRNA	Modstrings-internals
ModString	ModString
ModString,AsIs-method	ModString
ModString,character-method	ModString
ModString,factor-method	ModString
ModString,MaskedModString-method	ModString
ModString,ModString-method	ModString
ModString,XString-method	ModString
Modstrings	Modstrings
Modstrings-internals	Modstrings-internals
ModStringSet	ModStringSet
ModStringSet,ANY-method	ModStringSet
ModStringSet,AsIs-method	ModStringSet
ModStringSet,character-method	ModStringSet
ModStringSet,factor-method	ModStringSet
ModStringSet,list-method	ModStringSet
ModStringSet,missing-method	ModStringSet
ModStringSet,ModString-method	ModStringSet
ModStringSet,ModStringSet-method	ModStringSet
ModStringSet,ModStringViews-method	ModStringViews
ModStringSet-io	ModStringSet-io
ModStringSetList	ModStringSetList
ModStringViews	ModStringViews
MOD_RNA_DICT_MODOMICS	Modstrings-internals
MOD_RNA_DICT_TRNADB	Modstrings-internals
nomenclature	alphabet
nomenclature,ModString-method	alphabet
nomenclature,ModStringSet-method	alphabet
QualityScaledModDNAStringSet	QualityScaledModStringSet
QualityScaledModDNAStringSet-class	QualityScaledModStringSet
QualityScaledModRNAStringSet	QualityScaledModStringSet
QualityScaledModRNAStringSet-class	QualityScaledModStringSet
QualityScaledModStringSet	QualityScaledModStringSet
readModDNAStringSet	ModStringSet-io
readModRNAStringSet	ModStringSet-io
readQualityScaledModDNAStringSet	QualityScaledModStringSet
readQualityScaledModRNAStringSet	QualityScaledModStringSet
removeIncompatibleModifications	separate
removeIncompatibleModifications,GRanges,XString-method	separate
removeIncompatibleModifications,GRanges,XStringSet-method	separate
removeIncompatibleModifications,GRangesList,XStringSet-method	separate
replaceLetterAt	replaceLetterAt
replaceLetterAt,ModString-method	replaceLetterAt
replaceLetterAt,ModStringSet-method	replaceLetterAt
sanitizeFromModomics	sanitizeInput
sanitizeFromtRNAdb	sanitizeInput
sanitizeInput	sanitizeInput
separate	separate
separate,GRanges-method	separate
separate,GRangesList-method	separate
separate,ModString-method	separate
separate,ModStringSet-method	separate
seqtype,MaskedModString-method	MaskedModString
seqtype,ModDNAString-method	Modstrings-internals
seqtype,ModRNAString-method	Modstrings-internals
seqtype<-,ModString-method	Modstrings-internals
seqtype<-,ModStringSet-method	Modstrings-internals
shortName	alphabet
shortName,ModString-method	alphabet
shortName,ModStringSet-method	alphabet
show,ModStringSet-method	ModStringSet
show,ModStringViews-method	ModStringViews
show,QualityScaledModStringSet-method	QualityScaledModStringSet
Views,ModString-method	ModStringViews
writeModStringSet	ModStringSet-io
writeQualityScaledModStringSet	QualityScaledModStringSet
XString,ModString-method	Modstrings-internals
XStringSet,ModStringSet-method	Modstrings-internals
