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  "Package": "RNAmodR",
  "Type": "Package",
  "Title": "Detection of post-transcriptional modifications in high\nthroughput sequencing data",
  "Version": "1.27.0",
  "Date": "2025-09-23",
  "Authors@R": "c(person(\"Felix G.M.\", \n\"Ernst\",\nemail = \"felix.gm.ernst@outlook.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5064-0928\")),\nperson(\"Denis L.J.\",\n\"Lafontaine\",\nemail = \"denis.lafontaine@ulb.ac.be\",\nrole = c(\"ctb\", \"fnd\")))",
  "Description": "RNAmodR provides classes and workflows for\nloading/aggregation data from high througput sequencing aimed\nat detecting post-transcriptional modifications through\nanalysis of specific patterns. In addition, utilities are\nprovided to validate and visualize the results. The RNAmodR\npackage provides a core functionality from which specific\nanalysis strategies can be easily implemented as a seperate\npackage.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:22 UTC",
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  "Author": "Felix G.M. Ernst [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5064-0928>),\nDenis L.J. Lafontaine [ctb, fnd]",
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      "title": "Aggregate data per positions",
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        "aggregate,SequenceData-method",
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        "compareByCoord,ModifierSet,GRangesList-method",
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        "CoverageSequenceData",
        "CoverageSequenceData-class",
        "CoverageSequenceDataFrame",
        "CoverageSequenceDataFrame-class",
        "getData,CoverageSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method",
        "getDataTrack,CoverageSequenceData-method"
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      "title": "End5SequenceData/End3SequenceData/EndSequenceData",
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        "aggregateData,End5SequenceData-method",
        "aggregateData,EndSequenceData-method",
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        "End5SequenceDataFrame",
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        "getData,End5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method",
        "getData,EndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method",
        "getDataTrack,End3SequenceData-method",
        "getDataTrack,End5SequenceData-method",
        "getDataTrack,EndSequenceData-method"
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    {
      "page": "Modifier-class",
      "title": "The Modifier class",
      "topics": [
        "DNAModifier-class",
        "Modifier",
        "Modifier,BamFileList-method",
        "Modifier,character-method",
        "Modifier,list-method",
        "Modifier,SequenceData-method",
        "Modifier,SequenceDataList-method",
        "Modifier,SequenceDataSet-method",
        "Modifier-class",
        "RNAModifier-class"
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    {
      "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": [
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        "findMod,Modifier-method",
        "modifications",
        "modifications,Modifier-method",
        "modify",
        "modify,Modifier-method",
        "modify,ModifierSet-method"
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    },
    {
      "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": [
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        "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"
      ]
    },
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      "page": "PileupSequenceData-class",
      "title": "PileupSequenceData",
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        "getData,PileupSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method",
        "getDataTrack,PileupSequenceData-method",
        "PileupSequenceData",
        "PileupSequenceData-class",
        "PileupSequenceDataFrame",
        "PileupSequenceDataFrame-class",
        "pileupToCoverage",
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      ]
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      "page": "plotData",
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      "topics": [
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        "getDataTrack,Modifier-method",
        "getDataTrack,SequenceData-method",
        "getDataTrack,SequenceDataList-method",
        "getDataTrack,SequenceDataSet-method",
        "plotData",
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      "page": "plotROC",
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      "page": "RNAmodR",
      "title": "RNAmodR",
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        "RNAmodR"
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      "page": "RNAmodR-datasets",
      "title": "Example data in the RNAmodR package",
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        "e3sd",
        "e5sd",
        "esd",
        "msi",
        "ne3sd",
        "ne5sd",
        "pesd",
        "psd",
        "RNAmodR-datasets",
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        "sds"
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      "page": "RNAmodR-development",
      "title": "RNAmodR developments functions",
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        "constructModRanges,GRanges,DataFrame-method",
        "getData",
        "RNAmodR-development"
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      "page": "SequenceData-class",
      "title": "The SequenceData class",
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        "rbind,SequenceData-method",
        "SequenceData",
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      "page": "SequenceData-functions",
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      "page": "SequenceDataSet-class",
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      "page": "SequenceModDNAStringSetTrack-class",
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      "title": "RNAmodR: analyzing high throughput sequencing data for post-transcriptional RNA modification footprints",
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