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  "Title": "Methods for identifying small RNA loci from high-throughput\nsequencing data",
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  "Date": "2025-07-23",
  "Authors@R": "c(person(\"Thomas J.\", \"Hardcastle\", role = \"aut\"),\nperson(\"Samuel\", \"Granjeaud\", role = \"cre\", email = \"samuel.granjeaud@inserm.fr\", comment=c(ORCID=\"0000-0001-9245-1535\")))",
  "Description": "High-throughput sequencing technologies allow the\nproduction of large volumes of short sequences, which can be\naligned to the genome to create a set of matches to the genome.\nBy looking for regions of the genome which to which there are\nhigh densities of matches, we can infer a segmentation of the\ngenome into regions of biological significance. The methods in\nthis package allow the simultaneous segmentation of data from\nmultiple samples, taking into account replicate data, in order\nto create a consensus segmentation. This has obvious\napplications in a number of classes of sequencing experiments,\nparticularly in the discovery of small RNA loci and novel mRNA\ntranscriptome discovery.",
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  "biocViews": "MultipleComparison, Sequencing, Alignment,\nDifferentialExpression, QualityControl, DataImport",
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  "Author": "Thomas J. Hardcastle [aut],\nSamuel Granjeaud [cre] (ORCID: <https://orcid.org/0000-0001-9245-1535>)",
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      "title": "Segmentation of the genome based on multiple samples of high-throughput sequencing data.",
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        "segmentSeq"
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      "title": "Class \"alignmentClass\"",
      "topics": [
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        "alignmentClass-class",
        "cbind,alignmentClass-method",
        "dim,alignmentClass-method",
        "initialize,alignmentClass-method",
        "show,alignmentClass-method",
        "[,alignmentClass,ANY,ANY,ANY-method",
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        "[,alignmentClass,ANY-method",
        "[,alignmentClass-method"
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        "alignmentData-class",
        "cbind,alignmentData-method",
        "dim,alignmentData-method",
        "initialize,alignmentData-method",
        "show,alignmentData-method",
        "[,alignmentData,ANY,ANY,ANY-method",
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        "[,alignmentData,ANY-method",
        "[,alignmentData-method"
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      "title": "Class \"alignmentMeth\"",
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        "alignmentMeth-class",
        "cbind,alignmentMeth-method",
        "dim,alignmentMeth-method",
        "initialize,alignmentMeth-method",
        "show,alignmentMeth-method",
        "[,alignmentMeth,ANY,ANY,ANY-method",
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        "[,alignmentMeth,ANY-method",
        "[,alignmentMeth-method"
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    {
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      "title": "Computes and plots the average distribution of aligned reads (taken from an alignmentData object) or methylation (taken from an alignmentMeth object) over a set of coordinates (and optionally the surrounding regions).",
      "topics": [
        "averageProfiles",
        "plotAverageProfile"
      ]
    },
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      "title": "A method for defining a genome segment map by an empirical Bayesian classification method",
      "topics": [
        "classifySeg"
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      "title": "Identifies `chunks' of data within a set of aligned reads.",
      "topics": [
        "findChunks"
      ]
    },
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      "topics": [
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    {
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      "title": "Identifies overlaps between two sets of genomic coordinates",
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    },
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      "title": "Adjusts posterior likelihoods of differential expression by the likelihood that a locus is expressed.",
      "topics": [
        "givenExpression"
      ]
    },
    {
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      "title": "A (fast) heuristic method for creation of a genome segment map.",
      "topics": [
        "heuristicSeg"
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    },
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      "page": "hSL",
      "title": "Preprocessed 'lociData' object containing likelihoods of methylation at each locus.",
      "topics": [
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    },
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      "title": "Class \"lociData\"",
      "topics": [
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        "dim,lociData-method",
        "lociData",
        "lociData-class",
        "show,lociData-method",
        "[,lociData,ANY,ANY,ANY-method",
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        "[,lociData-method"
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      "topics": [
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        "[,methData,ANY-method",
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      "topics": [
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