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  "Title": "Finding differentially expressed unannotated genomic regions\nfrom RNA-seq data",
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  "Date": "2025-07-24",
  "Authors@R": "c(\nperson(\"Zytnicki\", \"Matthias\", email = \"matthias.zytnicki@inra.fr\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Gonzalez\", \"Ignacio\", role = \"aut\"))",
  "Description": "srnadiff is a package that finds differently expressed\nregions from RNA-seq data at base-resolution level without\nrelying on existing annotation. To do so, the package\nimplements the identify-then-annotate methodology that builds\non the idea of combining two pipelines approachs differential\nexpressed regions detection and differential expression\nquantification. It reads BAM files as input, and outputs a list\ndifferentially regions, together with the adjusted p-values.",
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  "Date/Publication": "2026-04-28 12:47:12 UTC",
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  "Author": "Zytnicki Matthias [aut, cre],\nGonzalez Ignacio [aut]",
  "Maintainer": "Zytnicki Matthias <matthias.zytnicki@inra.fr>",
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  "_created": "2026-11-01T14:25:15.000Z",
  "_published": "2026-11-01T18:05:53.460Z",
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      "source": "srnadiff.Rmd",
      "filename": "srnadiff.html",
      "title": "\"Finding differentially expressed unannotated genomic regions from RNA-seq data with srnadiff\"",
      "author": "Matthias Zytnicki, Ignacio González",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Version info",
        "Abstract",
        "Introduction",
        "Citing r Biocpkg(\"srnadiff\")",
        "How to get help for r Biocpkg(\"srnadiff\")",
        "Quick start",
        "Using r Biocpkg(\"srnadiff\")",
        "Installation",
        "Data overview",
        "Data preparation: the srnadiffExp object",
        "Content",
        "Adding an annotation",
        "Directionality",
        "The srnaExp object",
        "Read annotation",
        "Extraction of putative regions using an GTF annotation file",
        "Whole genome file annotation",
        "Extraction of precursor miRNAs using a miRBase-formatted GFF file",
        "Extraction of mature miRNAs using a miRBase-formatted GFF file",
        "Other format",
        "Performing sRNA-diff",
        "Working with the srnadiffExp object",
        "Extracting regions",
        "Data visualization",
        "Methods behind r Biocpkg(\"srnadiff\")",
        "Pre-processing data",
        "Methods to produce differentially expressed regions",
        "HMM method: hmm",
        "IR method: IR",
        "Naive method: naive",
        "Quantifying DERs",
        "General parameters",
        "Combination of strategies",
        "Choice of the strategies",
        "Quantification of the features",
        "Using an other method to compute adjusted p-values",
        "Misc",
        "Using several cores",
        "Troubleshooting",
        "Session information",
        "References"
      ],
      "created": "2017-02-22 13:51:13",
      "modified": "2024-12-18 14:47:42",
      "commits": 22
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