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  "Title": "Count summarization and normalization for RNA-Seq data",
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  "Maintainer": "Nicolas Delhomme <nicolas.delhomme@umu.se>",
  "Description": "Calculates the coverage of high-throughput short-reads\nagainst a genome of reference and summarizes it per feature of\ninterest (e.g. exon, gene, transcript). The data can be\nnormalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.",
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    "barcodePlot",
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    "fetchData",
    "fileName",
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    "geneCounts",
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    "getAnnotation",
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    "GRanges",
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    "paired",
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    "readCoverage",
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    "readLength",
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    "RnaSeqParam",
    "rowRanges",
    "RPKM",
    "seqinfo",
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    "seqlevels",
    "seqlevels<-",
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    "simpleRNASeq",
    "split",
    "srFilter",
    "SRFilterResult",
    "strand",
    "strand<-",
    "stranded",
    "strandProtocol",
    "SummarizedExperiment",
    "transcriptCounts",
    "tutorialData",
    "type",
    "unsafeAppend",
    "validate",
    "vignetteData",
    "width",
    "writeFastq",
    "writeGff3",
    "yieldSize"
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      "title": "Dataset included in the package",
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      "class": [
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      ],
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        "sex",
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        "ENA.run.accession",
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      ],
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      "table": true,
      "tojson": true
    }
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      "page": "easyRNASeq-AnnotParam-class",
      "title": "Class \"AnnotParam\"",
      "topics": [
        "AnnotParam class",
        "AnnotParam-class",
        "AnnotParamCharacter-class",
        "AnnotParamObject-class"
      ]
    },
    {
      "page": "easyRNASeq-BamParam-class",
      "title": "Class \"BamParam\"",
      "topics": [
        "BamParam class",
        "BamParam-class"
      ]
    },
    {
      "page": "basename-methods",
      "title": "Extend the basename function to display Rsamtools BamFile class basename",
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        "basename methods",
        "basename,BamFile-method",
        "basename,BamFileList-method"
      ]
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    {
      "page": "BiocFileCache-methods",
      "title": "Manages the data necessary for the examples using BiocFileCache",
      "topics": [
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        ".get_cache,ANY-method",
        "BiocFileCache methods",
        "fetchData",
        "fetchData,character-method",
        "tutorialData",
        "tutorialData,ANY-method",
        "vignetteData",
        "vignetteData,ANY-method"
      ]
    },
    {
      "page": "easyRNASeq-synthetic-transcripts",
      "title": "Methods to create synthetic transcripts",
      "topics": [
        "createSyntheticTranscripts",
        "createSyntheticTranscripts,AnnotParamCharacter-method",
        "createSyntheticTranscripts,character-method"
      ]
    },
    {
      "page": "easyRNASeq-defunct",
      "title": "The following function are defunct:         • 'easyRNASeq'         • 'fetchCoverage'         • 'fetchAnnotation'         • 'knownOrganisms'",
      "topics": [
        "Defunct functions",
        "easyRNASeq",
        "easyRNASeq,RNAseq-method",
        "fetchAnnotation",
        "fetchCoverage",
        "fetchCoverage,RNAseq-method",
        "knownOrganisms",
        "organismName",
        "organismName,RNAseq-method",
        "organismName<-",
        "organismName<-,RNAseq-method"
      ]
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    {
      "page": "easyRNASeq-accessors",
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        "chrSize",
        "chrSize,RNAseq-method",
        "chrSize<-",
        "chrSize<-,RNAseq,integer-method",
        "chrSize<-,RNAseq,list-method",
        "easyRNASeq accessors",
        "fileName",
        "fileName,RNAseq-method",
        "fileName<-",
        "fileName<-,RNAseq-method",
        "geneModel",
        "geneModel,RNAseq-method",
        "geneModel<-",
        "geneModel<-,RNAseq-method",
        "genomicAnnotation",
        "genomicAnnotation,RNAseq-method",
        "genomicAnnotation<-",
        "genomicAnnotation<-,RNAseq-method",
        "librarySize",
        "librarySize,RNAseq-method",
        "librarySize<-",
        "librarySize<-,RNAseq-method",
        "readCounts",
        "readCounts,RNAseq-method",
        "readCounts<-",
        "readCounts<-,RNAseq-method",
        "readCoverage",
        "readCoverage,RNAseq-method",
        "readCoverage<-",
        "readCoverage<-,RNAseq-method",
        "readIslands",
        "readIslands,RNAseq-method",
        "readIslands<-",
        "readIslands<-,RNAseq-method",
        "readLength",
        "readLength,RNAseq-method",
        "readLength<-",
        "readLength<-,RNAseq-method",
        "seqnames,RNAseq-method"
      ]
    },
    {
      "page": "easyRNASeq-annotation-methods",
      "title": "Get genic annotation from a gff3/gtf file or using biomaRt",
      "topics": [
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        "getAnnotation",
        "getAnnotation,AnnotParam-method"
      ]
    },
    {
      "page": "easyRNASeq-AnnotParam-accessors",
      "title": "Accessors for AnnotParam class",
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        "datasource",
        "datasource,AnnotParam-method",
        "easyRNASeq AnnotParam accessors",
        "type,AnnotParam-method"
      ]
    },
    {
      "page": "easyRNASeq-AnnotParam",
      "title": "AnnotParam constructor",
      "topics": [
        "AnnotParam",
        "AnnotParam,character-method",
        "AnnotParam,GRanges-method",
        "AnnotParam,missing-method",
        "easyRNASeq AnnotParam constructor"
      ]
    },
    {
      "page": "easyRNASeq-BamParam-accessors",
      "title": "Accessors for BamParam class",
      "topics": [
        "BamParam-accessors",
        "easyRNASeq BamParam accessors",
        "paired",
        "paired,BamParam-method",
        "stranded",
        "stranded,BamParam-method",
        "strandProtocol",
        "strandProtocol,BamParam-method",
        "yieldSize",
        "yieldSize,BamParam-method"
      ]
    },
    {
      "page": "easyRNASeq-BamParam",
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        "BamParam,ANY-method",
        "easyRNASeq BamParam constructor"
      ]
    },
    {
      "page": "easyRNASeq-correction-methods",
      "title": "easyRNASeq count table correction to RPKM",
      "topics": [
        "easyRNASeq correction methods",
        "RPKM",
        "RPKM,matrix,ANY,vector,vector-method",
        "RPKM,RNAseq,ANY,ANY,ANY-method",
        "RPKM,RNAseq-method"
      ]
    },
    {
      "page": "easyRNASeq-coverage-methods",
      "title": "Compute the coverage from a Short Read Alignment file",
      "topics": [
        "easyRNASeq coverage methods",
        "fetchCoverage-deprecated"
      ]
    },
    {
      "page": "easyRNASeq-defunct-annotation-methods",
      "title": "Defunct annotation function",
      "topics": [
        "easyRNASeq defunct annotation methods",
        "fetchAnnotation-defunct",
        "knownOrganisms-defunct"
      ]
    },
    {
      "page": "GenomicRanges-methods",
      "title": "Extension of the GenomicRanges package",
      "topics": [
        "colnames",
        "colnames,GRanges-method",
        "colnames,GRangesList-method",
        "easyRNASeq GenomicRanges package extension",
        "unsafeAppend",
        "unsafeAppend,GAlignments,GAlignments-method"
      ]
    },
    {
      "page": "easyRNASeq-island-methods",
      "title": "Identify expressed regions de-novo",
      "topics": [
        "easyRNASeq island methods",
        "findIslands",
        "findIslands,RNAseq-method"
      ]
    },
    {
      "page": "easyRNASeq-RnaSeqParam-accessors",
      "title": "Accessors for RnaSeqParam class",
      "topics": [
        "annotParam",
        "annotParam,RnaSeqParam-method",
        "bamParam",
        "bamParam,RnaSeqParam-method",
        "countBy",
        "countBy,RnaSeqParam-method",
        "datasource,RnaSeqParam-method",
        "easyRNASeq RnaSeqParam accessors",
        "paired,RnaSeqParam-method",
        "precision",
        "precision,RnaSeqParam-method",
        "RnaSeqParam-accessors",
        "stranded,RnaSeqParam-method",
        "strandProtocol,RnaSeqParam-method",
        "yieldSize,RnaSeqParam-method"
      ]
    },
    {
      "page": "easyRNASeq-RnaSeqParam",
      "title": "RnaSeqParam constructor",
      "topics": [
        "easyRNASeq RnaSeqParam constructor",
        "RnaSeqParam",
        "RnaSeqParam,ANY-method"
      ]
    },
    {
      "page": "easyRNASeq-summarization-methods",
      "title": "Count methods for RNAseq object",
      "topics": [
        "easyRNASeq summarization methods",
        "exonCounts",
        "exonCounts,RNAseq-method",
        "featureCounts",
        "featureCounts,RNAseq-method",
        "geneCounts",
        "geneCounts,RNAseq-method",
        "islandCounts",
        "islandCounts,RNAseq-method",
        "transcriptCounts",
        "transcriptCounts,RNAseq-method"
      ]
    },
    {
      "page": "easyRNASeq-datasets",
      "title": "Dataset included in the package",
      "topics": [
        "easyRNASeq-datasets",
        "RobinsonDelhomme2014"
      ]
    },
    {
      "page": "easyRNASeq-easyRNASeq",
      "title": "easyRNASeq method",
      "topics": [
        "easyRNASeq,character-method",
        "easyRNASeq-defunct"
      ]
    },
    {
      "page": "edgeR-methods",
      "title": "Extension for the edgeR package",
      "topics": [
        "edgeR additional methods",
        "plotNormalizationFactors",
        "plotNormalizationFactors,DGEList,character,character-method"
      ]
    },
    {
      "page": "file.exists-methods",
      "title": "Extend the file.exists function to check the path slot of a Rsamtools BamFile class for existence",
      "topics": [
        "file.exists",
        "file.exists methods",
        "file.exists,BamFile-method"
      ]
    },
    {
      "page": "genomeIntervals-methods",
      "title": "Extension for the genomeIntervals package",
      "topics": [
        "genomeIntervals additional methods",
        "type,Genome_intervals-method"
      ]
    },
    {
      "page": "easyRNASeq-BamFileList",
      "title": "Get a BamFileList from a list of filenames",
      "topics": [
        "getBamFileList",
        "getBamFileList,character,character-method",
        "getBamFileList,character,missing-method"
      ]
    },
    {
      "page": "IRanges-methods",
      "title": "Extension of the IRanges package",
      "topics": [
        "IRanges additional methods",
        "ranges",
        "ranges,RNAseq-method"
      ]
    },
    {
      "page": "parallel-methods",
      "title": "parallel additional methods",
      "topics": [
        "parallel additional methods",
        "parallelize",
        "parallelize,BamFileList,function-method",
        "parallelize,GRangesList,function-method",
        "parallelize,list,function-method",
        "parallelize,vector,function-method"
      ]
    },
    {
      "page": "print-methods",
      "title": "Pretty print the content of classes from the easyRNASeq package.",
      "topics": [
        "print",
        "print methods",
        "print,AnnotParam-method",
        "print,BamParam-method",
        "print,RNAseq-method",
        "print,RnaSeqParam-method"
      ]
    },
    {
      "page": "easyRNASeq-class",
      "title": "Class \"RNAseq\"",
      "topics": [
        "RNAseq",
        "RNAseq class",
        "RNAseq-class"
      ]
    },
    {
      "page": "easyRNASeq-RnaSeqParam-class",
      "title": "Class \"RnaSeqParam\"",
      "topics": [
        "RnaSeqParam class",
        "RnaSeqParam-class"
      ]
    },
    {
      "page": "ShortRead-methods",
      "title": "Methods extending the ShortRead package functionalities",
      "topics": [
        "alignData",
        "barcodePlot",
        "barcodePlot,AlignedRead-method",
        "barcodePlot,DNAStringSet-method",
        "barcodePlot,ShortReadQ-method",
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