A B C D E F G H I L M N P R S V misc
aggregate | Aggregate data per positions |
aggregate-method | Aggregate data per positions |
aggregateData | Aggregate data per positions |
aggregateData-method | CoverageSequenceData |
aggregateData-method | End5SequenceData/End3SequenceData/EndSequenceData |
aggregateData-method | Functions for ModInosine |
aggregateData-method | NormEnd5SequenceData/NormEnd3SequenceData |
aggregateData-method | PileupSequenceData |
aggregateData-method | ProtectedEndSequenceData |
aggregateData-method | Aggregate data per positions |
bamfiles | Modifier/ModifierSet functions |
bamfiles-method | Modifier/ModifierSet functions |
bamfiles-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
cbind-method | The SequenceData class |
cbind-method | The SequenceDataFrame class |
compare | Comparison of Samples |
compare-method | Comparison of Samples |
compareByCoord | Comparison of Samples |
compareByCoord-method | Comparison of Samples |
conditions-method | Modifier/ModifierSet functions |
conditions-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
constructModRanges | RNAmodR developments functions |
constructModRanges-method | RNAmodR developments functions |
CoverageSequenceData | CoverageSequenceData |
CoverageSequenceData-class | CoverageSequenceData |
CoverageSequenceDataFrame | CoverageSequenceData |
CoverageSequenceDataFrame-class | CoverageSequenceData |
csd | Example data in the RNAmodR package |
dataType | Modifier/ModifierSet functions |
dataType-method | Modifier/ModifierSet functions |
dataType-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
DNAModifier-class | The Modifier class |
e3sd | Example data in the RNAmodR package |
e5sd | Example data in the RNAmodR package |
End3SequenceData | End5SequenceData/End3SequenceData/EndSequenceData |
End3SequenceData-class | End5SequenceData/End3SequenceData/EndSequenceData |
End3SequenceDataFrame | End5SequenceData/End3SequenceData/EndSequenceData |
End3SequenceDataFrame-class | End5SequenceData/End3SequenceData/EndSequenceData |
End5SequenceData | End5SequenceData/End3SequenceData/EndSequenceData |
End5SequenceData-class | End5SequenceData/End3SequenceData/EndSequenceData |
End5SequenceDataFrame | End5SequenceData/End3SequenceData/EndSequenceData |
End5SequenceDataFrame-class | End5SequenceData/End3SequenceData/EndSequenceData |
EndSequenceData | End5SequenceData/End3SequenceData/EndSequenceData |
EndSequenceData-class | End5SequenceData/End3SequenceData/EndSequenceData |
EndSequenceDataFrame | End5SequenceData/End3SequenceData/EndSequenceData |
EndSequenceDataFrame-class | End5SequenceData/End3SequenceData/EndSequenceData |
esd | Example data in the RNAmodR package |
findMod | Searching for modifications in 'SequenceData' |
findMod-method | Functions for ModInosine |
findMod-method | Searching for modifications in 'SequenceData' |
getAggregateData | Aggregate data per positions |
getAggregateData-method | Aggregate data per positions |
getData | RNAmodR developments functions |
getData-method | CoverageSequenceData |
getData-method | End5SequenceData/End3SequenceData/EndSequenceData |
getData-method | NormEnd5SequenceData/NormEnd3SequenceData |
getData-method | PileupSequenceData |
getData-method | ProtectedEndSequenceData |
getData-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
getDataTrack | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
getDataTrack-method | CoverageSequenceData |
getDataTrack-method | End5SequenceData/End3SequenceData/EndSequenceData |
getDataTrack-method | Functions for ModInosine |
getDataTrack-method | NormEnd5SequenceData/NormEnd3SequenceData |
getDataTrack-method | PileupSequenceData |
getDataTrack-method | ProtectedEndSequenceData |
getDataTrack-method | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
hasAggregateData | Aggregate data per positions |
hasAggregateData-method | Aggregate data per positions |
ICE-Seq | ModInosine |
Inosine | ModInosine |
labelByCoord | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
labelByCoord-method | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
mainScore | Modifier/ModifierSet functions |
mainScore-method | Modifier/ModifierSet functions |
ModDNASequenceTrack | ModDNASequenceTrack |
ModDNASequenceTrack-class | ModDNASequenceTrack |
modifications | Searching for modifications in 'SequenceData' |
modifications-method | Modifier/ModifierSet functions |
modifications-method | Searching for modifications in 'SequenceData' |
Modifier | The Modifier class |
Modifier-class | The Modifier class |
Modifier-functions | Modifier/ModifierSet functions |
Modifier-method | The Modifier class |
ModifierInosine | ModInosine |
ModifierSet | The ModifierSet class |
ModifierSet-class | The ModifierSet class |
ModifierSet-method | The ModifierSet class |
modifierType | Modifier/ModifierSet functions |
modifierType-method | Modifier/ModifierSet functions |
modify | Searching for modifications in 'SequenceData' |
modify-method | Searching for modifications in 'SequenceData' |
ModInosine | ModInosine |
ModInosine-class | ModInosine |
ModInosine-functions | Functions for ModInosine |
ModInosine-internals | ModInosine internal functions |
ModRNASequenceTrack | ModRNASequenceTrack |
ModRNASequenceTrack-class | ModRNASequenceTrack |
ModSetInosine | ModInosine |
ModSetInosine-class | ModInosine |
modType | Modifier/ModifierSet functions |
modType-method | Modifier/ModifierSet functions |
msi | Example data in the RNAmodR package |
names-method | Modifier/ModifierSet functions |
names-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
ne3sd | Example data in the RNAmodR package |
ne5sd | Example data in the RNAmodR package |
NormEnd3SequenceData | NormEnd5SequenceData/NormEnd3SequenceData |
NormEnd3SequenceData-class | NormEnd5SequenceData/NormEnd3SequenceData |
NormEnd3SequenceDataFrame | NormEnd5SequenceData/NormEnd3SequenceData |
NormEnd3SequenceDataFrame-class | NormEnd5SequenceData/NormEnd3SequenceData |
NormEnd5SequenceData | NormEnd5SequenceData/NormEnd3SequenceData |
NormEnd5SequenceData-class | NormEnd5SequenceData/NormEnd3SequenceData |
NormEnd5SequenceDataFrame | NormEnd5SequenceData/NormEnd3SequenceData |
NormEnd5SequenceDataFrame-class | NormEnd5SequenceData/NormEnd3SequenceData |
NormEndSequenceData-class | NormEnd5SequenceData/NormEnd3SequenceData |
pesd | Example data in the RNAmodR package |
PileupSequenceData | PileupSequenceData |
PileupSequenceData-class | PileupSequenceData |
PileupSequenceDataFrame | PileupSequenceData |
PileupSequenceDataFrame-class | PileupSequenceData |
pileupToCoverage | PileupSequenceData |
pileupToCoverage-method | PileupSequenceData |
plotCompare | Comparison of Samples |
plotCompare-method | Comparison of Samples |
plotCompareByCoord | Comparison of Samples |
plotCompareByCoord-method | Comparison of Samples |
plotData | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
plotData-method | Functions for ModInosine |
plotData-method | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
plotDataByCoord | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
plotDataByCoord-method | Functions for ModInosine |
plotDataByCoord-method | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
plotROC | ROCR functions for 'Modifier' and 'ModifierSet' objects |
plotROC-method | ROCR functions for 'Modifier' and 'ModifierSet' objects |
ProtectedEndSequenceData | ProtectedEndSequenceData |
ProtectedEndSequenceData-class | ProtectedEndSequenceData |
ProtectedEndSequenceDataFrame | ProtectedEndSequenceData |
ProtectedEndSequenceDataFrame-class | ProtectedEndSequenceData |
psd | Example data in the RNAmodR package |
ranges-method | Modifier/ModifierSet functions |
ranges-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
rbind-method | The SequenceData class |
replicates | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
replicates-method | Modifier/ModifierSet functions |
replicates-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
RNAModifier-class | The Modifier class |
RNAmodR | RNAmodR |
RNAmodR-datasets | Example data in the RNAmodR package |
RNAmodR-development | RNAmodR developments functions |
RNASequenceTrack | RNASequenceTrack |
RNASequenceTrack-class | RNASequenceTrack |
sdl | Example data in the RNAmodR package |
sds | Example data in the RNAmodR package |
seqinfo-method | Modifier/ModifierSet functions |
seqinfo-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
seqtype-method | Modifier/ModifierSet functions |
seqtype-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
seqtype<--method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
SequenceData | The SequenceData class |
sequenceData | Modifier/ModifierSet functions |
SequenceData-class | The SequenceData class |
SequenceData-functions | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
SequenceData-method | The SequenceData class |
sequenceData-method | Modifier/ModifierSet functions |
SequenceDataFrame | The SequenceDataFrame class |
SequenceDataFrame-class | The SequenceDataFrame class |
SequenceDataList | The SequenceDataList class |
SequenceDataList-class | The SequenceDataList class |
SequenceDataSet | The SequenceDataSet class |
SequenceDataSet-class | The SequenceDataSet class |
SequenceDFrame-class | The SequenceDataFrame class |
sequences | Modifier/ModifierSet functions |
sequences-method | Modifier/ModifierSet functions |
sequences-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
settings | Settings for 'Modifier' objects |
settings-method | Settings for 'Modifier' objects |
settings<- | Settings for 'Modifier' objects |
settings<--method | Functions for ModInosine |
settings<--method | Settings for 'Modifier' objects |
show-method | Modifier/ModifierSet functions |
show-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
subset-method | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
subsetByCoord | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
subsetByCoord-method | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
validAggregate | Modifier/ModifierSet functions |
validAggregate-method | Modifier/ModifierSet functions |
validModification | Modifier/ModifierSet functions |
validModification-method | Modifier/ModifierSet functions |
.dataTracks-method | ModInosine internal functions |
[-method | The SequenceDataFrame class |