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"Modifier,SequenceDataList-method", "Modifier,SequenceDataSet-method", "Modifier-class", "RNAModifier-class" ] }, { "page": "Modifier-functions", "title": "Modifier/ModifierSet functions", "topics": [ "bamfiles", "bamfiles,Modifier-method", "bamfiles,ModifierSet-method", "conditions,Modifier-method", "conditions,ModifierSet-method", "dataType", "dataType,Modifier-method", "dataType,ModifierSet-method", "mainScore", "mainScore,Modifier-method", "mainScore,ModifierSet-method", "modifications,ModifierSet-method", "Modifier-functions", "modifierType", "modifierType,Modifier-method", "modifierType,ModifierSet-method", "modType", "modType,Modifier-method", "modType,ModifierSet-method", "names,Modifier-method", "ranges,Modifier-method", "ranges,ModifierSet-method", "replicates,Modifier-method", "replicates,ModifierSet-method", "seqinfo,Modifier-method", "seqinfo,ModifierSet-method", "seqtype,Modifier-method", "seqtype,ModifierSet-method", "sequenceData", "sequenceData,Modifier-method", "sequences", "sequences,Modifier-method", "sequences,ModifierSet-method", "show,Modifier-method", "show,ModifierSet-method", "validAggregate", "validAggregate,Modifier-method", "validModification", "validModification,Modifier-method" ] }, { "page": "ModifierSet-class", "title": "The ModifierSet class", "topics": [ "ModifierSet", "ModifierSet,BamFileList-method", "ModifierSet,character-method", "ModifierSet,list-method", "ModifierSet,Modifier-method", "ModifierSet-class" ] }, { "page": "modify", "title": "Searching for modifications in 'SequenceData'", "topics": [ "findMod", "findMod,Modifier-method", "modifications", "modifications,Modifier-method", "modify", "modify,Modifier-method", "modify,ModifierSet-method" ] }, { "page": "ModInosine", "title": "ModInosine", "topics": [ "ICE-Seq", "Inosine", "ModifierInosine", "ModInosine", "ModInosine-class", "ModSetInosine", "ModSetInosine-class" ] }, { "page": "ModInosine-functions", "title": "Functions for ModInosine", "topics": [ "aggregateData,ModInosine-method", "findMod,ModInosine-method", "getDataTrack,ModInosine-method", "ModInosine-functions", "plotData,ModInosine-method", "plotData,ModSetInosine-method", "plotDataByCoord,ModInosine,GRanges-method", "plotDataByCoord,ModSetInosine,GRanges-method", "settings<-,ModInosine-method" ] }, { "page": "ModInosine-internals", "title": "ModInosine internal functions", "topics": [ ".dataTracks,ModInosine,GRanges,GRanges,XString-method", "ModInosine-internals" ] }, { "page": "NormEndSequenceData-class", "title": "NormEnd5SequenceData/NormEnd3SequenceData", "topics": [ "aggregateData,NormEnd3SequenceData-method", "aggregateData,NormEnd5SequenceData-method", "getData,NormEnd3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method", "getData,NormEnd5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method", "getDataTrack,NormEnd3SequenceData-method", "getDataTrack,NormEnd5SequenceData-method", "NormEnd3SequenceData", "NormEnd3SequenceData-class", "NormEnd3SequenceDataFrame", "NormEnd3SequenceDataFrame-class", "NormEnd5SequenceData", "NormEnd5SequenceData-class", "NormEnd5SequenceDataFrame", "NormEnd5SequenceDataFrame-class", "NormEndSequenceData-class" ] }, { "page": "PileupSequenceData-class", "title": "PileupSequenceData", "topics": [ "aggregateData,PileupSequenceData-method", "getData,PileupSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method", "getDataTrack,PileupSequenceData-method", "PileupSequenceData", "PileupSequenceData-class", "PileupSequenceDataFrame", "PileupSequenceDataFrame-class", "pileupToCoverage", "pileupToCoverage,PileupSequenceData-method" ] }, { "page": "plotData", "title": "Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object.", "topics": [ "getDataTrack", "getDataTrack,Modifier-method", "getDataTrack,SequenceData-method", "getDataTrack,SequenceDataList-method", "getDataTrack,SequenceDataSet-method", "plotData", "plotData,Modifier-method", "plotData,ModifierSet-method", "plotData,SequenceData-method", "plotData,SequenceDataList-method", "plotData,SequenceDataSet-method", "plotDataByCoord", "plotDataByCoord,Modifier,GRanges-method", "plotDataByCoord,ModifierSet,GRanges-method", "plotDataByCoord,SequenceData,GRanges-method", "plotDataByCoord,SequenceDataList,GRanges-method", "plotDataByCoord,SequenceDataSet,GRanges-method" ] }, { "page": "plotROC", "title": "ROCR functions for 'Modifier' and 'ModifierSet' objects", "topics": [ "plotROC", "plotROC,Modifier-method", "plotROC,ModifierSet-method" ] }, { "page": "ProtectedEndSequenceData-class", "title": "ProtectedEndSequenceData", "topics": [ "aggregateData,ProtectedEndSequenceData-method", "getData,ProtectedEndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method", "getDataTrack,ProtectedEndSequenceData-method", "ProtectedEndSequenceData", "ProtectedEndSequenceData-class", "ProtectedEndSequenceDataFrame", "ProtectedEndSequenceDataFrame-class" ] }, { "page": "RNAmodR", "title": "RNAmodR", "topics": [ "RNAmodR" ] }, { "page": "RNAmodR-datasets", "title": "Example data in the RNAmodR package", "topics": [ "csd", "e3sd", "e5sd", "esd", "msi", "ne3sd", "ne5sd", "pesd", "psd", "RNAmodR-datasets", "sdl", "sds" ] }, { "page": "RNAmodR-development", "title": "RNAmodR developments functions", "topics": [ "constructModRanges", "constructModRanges,GRanges,DataFrame-method", "getData", "RNAmodR-development" ] }, { "page": "SequenceData-class", "title": "The SequenceData class", "topics": [ "cbind,SequenceData-method", "rbind,SequenceData-method", "SequenceData", "SequenceData,character,BSgenome-method", "SequenceData,character,character-method", "SequenceData,character,FaFile-method", "SequenceData,GFF3File,BSgenome-method", "SequenceData,GFF3File,character-method", "SequenceData,GFF3File,FaFile-method", "SequenceData,GRangesList,BSgenome-method", "SequenceData,GRangesList,character-method", "SequenceData,GRangesList,FaFile-method", "SequenceData,TxDb,BSgenome-method", "SequenceData,TxDb,character-method", "SequenceData,TxDb,FaFile-method", "SequenceData-class" ] }, { "page": "SequenceData-functions", "title": "SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions", "topics": [ "bamfiles,SequenceData-method", "bamfiles,SequenceDataFrame-method", "bamfiles,SequenceDataList-method", "bamfiles,SequenceDataSet-method", "conditions,SequenceData-method", "conditions,SequenceDataFrame-method", "conditions,SequenceDataList-method", "conditions,SequenceDataSet-method", "dataType,SequenceData-method", "dataType,SequenceDataFrame-method", "getData,SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method", "names,SequenceDataList-method", "names,SequenceDataSet-method", "ranges,SequenceData-method", "ranges,SequenceDataFrame-method", "ranges,SequenceDataList-method", "ranges,SequenceDataSet-method", "replicates", "replicates,SequenceData-method", "replicates,SequenceDataFrame-method", "replicates,SequenceDataList-method", "replicates,SequenceDataSet-method", "seqinfo,SequenceData-method", "seqinfo,SequenceDataFrame-method", "seqinfo,SequenceDataList-method", "seqinfo,SequenceDataSet-method", "seqtype,SequenceData-method", "seqtype,SequenceDataFrame-method", "seqtype,SequenceDataList-method", "seqtype,SequenceDataSet-method", "seqtype<-,SequenceData-method", "seqtype<-,SequenceDataFrame-method", "seqtype<-,SequenceDataList-method", "seqtype<-,SequenceDataSet-method", "SequenceData-functions", "sequences,SequenceData-method", "sequences,SequenceDataFrame-method", "sequences,SequenceDataList-method", "sequences,SequenceDataSet-method", "show,SequenceData-method", "show,SequenceDataFrame-method", "show,SequenceDataList-method", "show,SequenceDataSet-method" ] }, { "page": "SequenceDataFrame-class", "title": "The SequenceDataFrame class", "topics": [ "cbind,SequenceDataFrame-method", "SequenceDataFrame", "SequenceDataFrame-class", "SequenceDFrame-class", "[,SequenceDataFrame,ANY,ANY,ANY-method" ] }, { "page": "SequenceDataList-class", "title": "The SequenceDataList class", "topics": [ "SequenceDataList", "SequenceDataList-class" ] }, { "page": "SequenceDataSet-class", "title": "The SequenceDataSet class", "topics": [ "SequenceDataSet", "SequenceDataSet-class" ] }, { "page": "SequenceModDNAStringSetTrack-class", "title": "ModDNASequenceTrack", "topics": [ "ModDNASequenceTrack", "seqlevels,SequenceModDNAStringSetTrack-method", "seqnames,SequenceModDNAStringSetTrack-method", "SequenceModDNAStringSetTrack", "SequenceModDNAStringSetTrack-class" ] }, { "page": "SequenceModRNAStringSetTrack-class", "title": "ModRNASequenceTrack", "topics": [ "ModRNASequenceTrack", "seqlevels,SequenceModRNAStringSetTrack-method", "seqnames,SequenceModRNAStringSetTrack-method", "SequenceModRNAStringSetTrack", "SequenceModRNAStringSetTrack-class" ] }, { "page": "settings", "title": "Settings for 'Modifier' objects", "topics": [ 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