.dataTracks,ModInosine,GRanges,GRanges,XString-method	ModInosine-internals
.getData	RNAmodR-internals
aggregate	aggregate
aggregate,Modifier-method	aggregate
aggregate,ModifierSet-method	aggregate
aggregate,SequenceData-method	aggregate
aggregate,SequenceDataList-method	aggregate
aggregate,SequenceDataSet-method	aggregate
aggregateData	aggregate
aggregateData,CoverageSequenceData-method	CoverageSequenceData-class
aggregateData,End3SequenceData-method	EndSequenceData-class
aggregateData,End5SequenceData-method	EndSequenceData-class
aggregateData,EndSequenceData-method	EndSequenceData-class
aggregateData,Modifier-method	aggregate
aggregateData,ModInosine-method	ModInosine-functions
aggregateData,NormEnd3SequenceData-method	NormEndSequenceData-class
aggregateData,NormEnd5SequenceData-method	NormEndSequenceData-class
aggregateData,PileupSequenceData-method	PileupSequenceData-class
aggregateData,ProtectedEndSequenceData-method	ProtectedEndSequenceData-class
aggregateData,SequenceData-method	aggregate
bamfiles	Modifier-functions
bamfiles,Modifier-method	Modifier-functions
bamfiles,ModifierSet-method	Modifier-functions
bamfiles,SequenceData-method	SequenceData-functions
bamfiles,SequenceDataFrame-method	SequenceData-functions
bamfiles,SequenceDataList-method	SequenceData-functions
bamfiles,SequenceDataSet-method	SequenceData-functions
cbind,SequenceData-method	SequenceData-class
cbind,SequenceDataFrame-method	SequenceDataFrame-class
compare	compareByCoord
compare,ModifierSet-method	compareByCoord
compareByCoord	compareByCoord
compareByCoord,ModifierSet,GRanges-method	compareByCoord
compareByCoord,ModifierSet,GRangesList-method	compareByCoord
conditions,Modifier-method	Modifier-functions
conditions,ModifierSet-method	Modifier-functions
conditions,SequenceData-method	SequenceData-functions
conditions,SequenceDataFrame-method	SequenceData-functions
conditions,SequenceDataList-method	SequenceData-functions
conditions,SequenceDataSet-method	SequenceData-functions
constructModRanges	RNAmodR-development
constructModRanges,GRanges,DataFrame-method	RNAmodR-development
CoverageSequenceData	CoverageSequenceData-class
CoverageSequenceData-class	CoverageSequenceData-class
CoverageSequenceDataFrame	CoverageSequenceData-class
CoverageSequenceDataFrame-class	CoverageSequenceData-class
csd	RNAmodR-datasets
dataType	Modifier-functions
dataType,Modifier-method	Modifier-functions
dataType,ModifierSet-method	Modifier-functions
dataType,SequenceData-method	SequenceData-functions
dataType,SequenceDataFrame-method	SequenceData-functions
DNAModifier-class	Modifier-class
e3sd	RNAmodR-datasets
e5sd	RNAmodR-datasets
End3SequenceData	EndSequenceData-class
End3SequenceData-class	EndSequenceData-class
End3SequenceDataFrame	EndSequenceData-class
End3SequenceDataFrame-class	EndSequenceData-class
End5SequenceData	EndSequenceData-class
End5SequenceData-class	EndSequenceData-class
End5SequenceDataFrame	EndSequenceData-class
End5SequenceDataFrame-class	EndSequenceData-class
EndSequenceData	EndSequenceData-class
EndSequenceData-class	EndSequenceData-class
EndSequenceDataFrame	EndSequenceData-class
EndSequenceDataFrame-class	EndSequenceData-class
esd	RNAmodR-datasets
findMod	modify
findMod,Modifier-method	modify
findMod,ModInosine-method	ModInosine-functions
getAggregateData	aggregate
getAggregateData,Modifier-method	aggregate
getData	RNAmodR-development
getData,CoverageSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	CoverageSequenceData-class
getData,End3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	EndSequenceData-class
getData,End5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	EndSequenceData-class
getData,EndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	EndSequenceData-class
getData,NormEnd3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	NormEndSequenceData-class
getData,NormEnd5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	NormEndSequenceData-class
getData,PileupSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	PileupSequenceData-class
getData,ProtectedEndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	ProtectedEndSequenceData-class
getData,SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method	SequenceData-functions
getDataTrack	plotData
getDataTrack,CoverageSequenceData-method	CoverageSequenceData-class
getDataTrack,End3SequenceData-method	EndSequenceData-class
getDataTrack,End5SequenceData-method	EndSequenceData-class
getDataTrack,EndSequenceData-method	EndSequenceData-class
getDataTrack,Modifier-method	plotData
getDataTrack,ModInosine-method	ModInosine-functions
getDataTrack,NormEnd3SequenceData-method	NormEndSequenceData-class
getDataTrack,NormEnd5SequenceData-method	NormEndSequenceData-class
getDataTrack,PileupSequenceData-method	PileupSequenceData-class
getDataTrack,ProtectedEndSequenceData-method	ProtectedEndSequenceData-class
getDataTrack,SequenceData-method	plotData
getDataTrack,SequenceDataList-method	plotData
getDataTrack,SequenceDataSet-method	plotData
getListElement,SequenceDataList-method	RNAmodR-internals
getListElement,SequenceDataSet-method	RNAmodR-internals
hasAggregateData	aggregate
hasAggregateData,Modifier-method	aggregate
ICE-Seq	ModInosine
Inosine	ModInosine
labelByCoord	subsetByCoord
labelByCoord,Modifier,GRanges-method	subsetByCoord
labelByCoord,Modifier,GRangesList-method	subsetByCoord
labelByCoord,ModifierSet,GRanges-method	subsetByCoord
labelByCoord,ModifierSet,GRangesList-method	subsetByCoord
labelByCoord,SequenceData,GRanges-method	subsetByCoord
labelByCoord,SequenceData,GRangesList-method	subsetByCoord
labelByCoord,SequenceDataList,GRanges-method	subsetByCoord
labelByCoord,SequenceDataList,GRangesList-method	subsetByCoord
labelByCoord,SequenceDataSet,GRanges-method	subsetByCoord
labelByCoord,SequenceDataSet,GRangesList-method	subsetByCoord
labelByCoord,SplitDataFrameList,GRanges-method	RNAmodR-internals
mainScore	Modifier-functions
mainScore,Modifier-method	Modifier-functions
mainScore,ModifierSet-method	Modifier-functions
ModDNASequenceTrack	SequenceModDNAStringSetTrack-class
modifications	modify
modifications,Modifier-method	modify
modifications,ModifierSet-method	Modifier-functions
Modifier	Modifier-class
Modifier,BamFileList-method	Modifier-class
Modifier,character-method	Modifier-class
Modifier,list-method	Modifier-class
Modifier,SequenceData-method	Modifier-class
Modifier,SequenceDataList-method	Modifier-class
Modifier,SequenceDataSet-method	Modifier-class
Modifier-class	Modifier-class
Modifier-functions	Modifier-functions
ModifierInosine	ModInosine
ModifierSet	ModifierSet-class
ModifierSet,BamFileList-method	ModifierSet-class
ModifierSet,character-method	ModifierSet-class
ModifierSet,list-method	ModifierSet-class
ModifierSet,Modifier-method	ModifierSet-class
ModifierSet-class	ModifierSet-class
modifierType	Modifier-functions
modifierType,Modifier-method	Modifier-functions
modifierType,ModifierSet-method	Modifier-functions
modify	modify
modify,Modifier-method	modify
modify,ModifierSet-method	modify
ModInosine	ModInosine
ModInosine-class	ModInosine
ModInosine-functions	ModInosine-functions
ModInosine-internals	ModInosine-internals
ModRNASequenceTrack	SequenceModRNAStringSetTrack-class
ModSetInosine	ModInosine
ModSetInosine-class	ModInosine
modType	Modifier-functions
modType,Modifier-method	Modifier-functions
modType,ModifierSet-method	Modifier-functions
msi	RNAmodR-datasets
names,Modifier-method	Modifier-functions
names,SequenceDataList-method	SequenceData-functions
names,SequenceDataSet-method	SequenceData-functions
ne3sd	RNAmodR-datasets
ne5sd	RNAmodR-datasets
NormEnd3SequenceData	NormEndSequenceData-class
NormEnd3SequenceData-class	NormEndSequenceData-class
NormEnd3SequenceDataFrame	NormEndSequenceData-class
NormEnd3SequenceDataFrame-class	NormEndSequenceData-class
NormEnd5SequenceData	NormEndSequenceData-class
NormEnd5SequenceData-class	NormEndSequenceData-class
NormEnd5SequenceDataFrame	NormEndSequenceData-class
NormEnd5SequenceDataFrame-class	NormEndSequenceData-class
NormEndSequenceData-class	NormEndSequenceData-class
parallel_slot_names,SequenceDataList-method	RNAmodR-internals
parallel_slot_names,SequenceDataSet-method	RNAmodR-internals
pesd	RNAmodR-datasets
PileupSequenceData	PileupSequenceData-class
PileupSequenceData-class	PileupSequenceData-class
PileupSequenceDataFrame	PileupSequenceData-class
PileupSequenceDataFrame-class	PileupSequenceData-class
pileupToCoverage	PileupSequenceData-class
pileupToCoverage,PileupSequenceData-method	PileupSequenceData-class
plotCompare	compareByCoord
plotCompare,ModifierSet-method	compareByCoord
plotCompareByCoord	compareByCoord
plotCompareByCoord,ModifierSet,GRanges-method	compareByCoord
plotCompareByCoord,ModifierSet,GRangesList-method	compareByCoord
plotData	plotData
plotData,Modifier-method	plotData
plotData,ModifierSet-method	plotData
plotData,ModInosine-method	ModInosine-functions
plotData,ModSetInosine-method	ModInosine-functions
plotData,SequenceData-method	plotData
plotData,SequenceDataList-method	plotData
plotData,SequenceDataSet-method	plotData
plotDataByCoord	plotData
plotDataByCoord,Modifier,GRanges-method	plotData
plotDataByCoord,ModifierSet,GRanges-method	plotData
plotDataByCoord,ModInosine,GRanges-method	ModInosine-functions
plotDataByCoord,ModSetInosine,GRanges-method	ModInosine-functions
plotDataByCoord,SequenceData,GRanges-method	plotData
plotDataByCoord,SequenceDataList,GRanges-method	plotData
plotDataByCoord,SequenceDataSet,GRanges-method	plotData
plotROC	plotROC
plotROC,Modifier-method	plotROC
plotROC,ModifierSet-method	plotROC
ProtectedEndSequenceData	ProtectedEndSequenceData-class
ProtectedEndSequenceData-class	ProtectedEndSequenceData-class
ProtectedEndSequenceDataFrame	ProtectedEndSequenceData-class
ProtectedEndSequenceDataFrame-class	ProtectedEndSequenceData-class
psd	RNAmodR-datasets
ranges,Modifier-method	Modifier-functions
ranges,ModifierSet-method	Modifier-functions
ranges,SequenceData-method	SequenceData-functions
ranges,SequenceDataFrame-method	SequenceData-functions
ranges,SequenceDataList-method	SequenceData-functions
ranges,SequenceDataSet-method	SequenceData-functions
rbind,SequenceData-method	SequenceData-class
replicates	SequenceData-functions
replicates,Modifier-method	Modifier-functions
replicates,ModifierSet-method	Modifier-functions
replicates,SequenceData-method	SequenceData-functions
replicates,SequenceDataFrame-method	SequenceData-functions
replicates,SequenceDataList-method	SequenceData-functions
replicates,SequenceDataSet-method	SequenceData-functions
RNAModifier-class	Modifier-class
RNAmodR	RNAmodR
RNAmodR-datasets	RNAmodR-datasets
RNAmodR-development	RNAmodR-development
RNAmodR-internals	RNAmodR-internals
sdl	RNAmodR-datasets
sds	RNAmodR-datasets
seqinfo,Modifier-method	Modifier-functions
seqinfo,ModifierSet-method	Modifier-functions
seqinfo,SequenceData-method	SequenceData-functions
seqinfo,SequenceDataFrame-method	SequenceData-functions
seqinfo,SequenceDataList-method	SequenceData-functions
seqinfo,SequenceDataSet-method	SequenceData-functions
seqlevels,SequenceModDNAStringSetTrack-method	SequenceModDNAStringSetTrack-class
seqlevels,SequenceModRNAStringSetTrack-method	SequenceModRNAStringSetTrack-class
seqnames,SequenceModDNAStringSetTrack-method	SequenceModDNAStringSetTrack-class
seqnames,SequenceModRNAStringSetTrack-method	SequenceModRNAStringSetTrack-class
seqtype,Modifier-method	Modifier-functions
seqtype,ModifierSet-method	Modifier-functions
seqtype,SequenceData-method	SequenceData-functions
seqtype,SequenceDataFrame-method	SequenceData-functions
seqtype,SequenceDataList-method	SequenceData-functions
seqtype,SequenceDataSet-method	SequenceData-functions
seqtype<-,SequenceData-method	SequenceData-functions
seqtype<-,SequenceDataFrame-method	SequenceData-functions
seqtype<-,SequenceDataList-method	SequenceData-functions
seqtype<-,SequenceDataSet-method	SequenceData-functions
SequenceData	SequenceData-class
sequenceData	Modifier-functions
SequenceData,character,BSgenome-method	SequenceData-class
SequenceData,character,character-method	SequenceData-class
SequenceData,character,FaFile-method	SequenceData-class
SequenceData,GFF3File,BSgenome-method	SequenceData-class
SequenceData,GFF3File,character-method	SequenceData-class
SequenceData,GFF3File,FaFile-method	SequenceData-class
SequenceData,GRangesList,BSgenome-method	SequenceData-class
SequenceData,GRangesList,character-method	SequenceData-class
SequenceData,GRangesList,FaFile-method	SequenceData-class
sequenceData,Modifier-method	Modifier-functions
SequenceData,TxDb,BSgenome-method	SequenceData-class
SequenceData,TxDb,character-method	SequenceData-class
SequenceData,TxDb,FaFile-method	SequenceData-class
SequenceData-class	SequenceData-class
SequenceData-functions	SequenceData-functions
SequenceDataFrame	SequenceDataFrame-class
SequenceDataFrame-class	SequenceDataFrame-class
SequenceDataList	SequenceDataList-class
SequenceDataList-class	SequenceDataList-class
SequenceDataSet	SequenceDataSet-class
SequenceDataSet-class	SequenceDataSet-class
SequenceDFrame-class	SequenceDataFrame-class
SequenceModDNAStringSetTrack	SequenceModDNAStringSetTrack-class
SequenceModDNAStringSetTrack-class	SequenceModDNAStringSetTrack-class
SequenceModRNAStringSetTrack	SequenceModRNAStringSetTrack-class
SequenceModRNAStringSetTrack-class	SequenceModRNAStringSetTrack-class
sequences	Modifier-functions
sequences,Modifier-method	Modifier-functions
sequences,ModifierSet-method	Modifier-functions
sequences,SequenceData-method	SequenceData-functions
sequences,SequenceDataFrame-method	SequenceData-functions
sequences,SequenceDataList-method	SequenceData-functions
sequences,SequenceDataSet-method	SequenceData-functions
settings	settings
settings,Modifier-method	settings
settings,ModifierSet-method	settings
settings<-	settings
settings<-,Modifier-method	settings
settings<-,ModifierSet-method	settings
settings<-,ModInosine-method	ModInosine-functions
show,Modifier-method	Modifier-functions
show,ModifierSet-method	Modifier-functions
show,SequenceData-method	SequenceData-functions
show,SequenceDataFrame-method	SequenceData-functions
show,SequenceDataList-method	SequenceData-functions
show,SequenceDataSet-method	SequenceData-functions
stats	stats
stats,Modifier,missing-method	stats
stats,ModifierSet,missing-method	stats
stats,SequenceData,BamFile-method	stats
stats,SequenceData,BamFileList-method	stats
subset,Modifier-method	RNAmodR-internals
subset,ModifierSet-method	subsetByCoord
subset,SequenceData-method	subsetByCoord
subset,SequenceDataList-method	subsetByCoord
subset,SequenceDataSet-method	subsetByCoord
subsetByCoord	subsetByCoord
subsetByCoord,Modifier,GRanges-method	subsetByCoord
subsetByCoord,Modifier,GRangesList-method	subsetByCoord
subsetByCoord,ModifierSet,GRanges-method	subsetByCoord
subsetByCoord,ModifierSet,GRangesList-method	subsetByCoord
subsetByCoord,SequenceData,GRanges-method	subsetByCoord
subsetByCoord,SequenceData,GRangesList-method	subsetByCoord
subsetByCoord,SequenceDataList,GRanges-method	subsetByCoord
subsetByCoord,SequenceDataList,GRangesList-method	subsetByCoord
subsetByCoord,SequenceDataSet,GRanges-method	subsetByCoord
subsetByCoord,SequenceDataSet,GRangesList-method	subsetByCoord
subsetByCoord,SplitDataFrameList,GRanges-method	subsetByCoord
validAggregate	Modifier-functions
validAggregate,Modifier-method	Modifier-functions
validModification	Modifier-functions
validModification,Modifier-method	Modifier-functions
[,SequenceDataFrame,ANY,ANY,ANY-method	SequenceDataFrame-class
