{
  "_id": "6a1ad6691d7bb097a09e5b2e",
  "Package": "DEXSeq",
  "Version": "1.59.0",
  "Title": "Inference of differential exon usage in RNA-Seq",
  "Authors@R": "c(\nperson(\"Simon\", \"Anders\", email = \"sanders@fs.tum.de\", role = \"aut\"),\nperson(\"Alejandro\", \"Reyes\", email = \"alejandro.reyes.ds@gmail.com\", role = c(\"aut\", \"ccp\"),\ncomment = \"Maintainer until 2026.\"),\nperson(\"Hugo\", \"Gruson\", email = \"hugo.gruson@embl.de\", role = \"cre\")\n)",
  "Description": "The package is focused on finding differential exon usage\nusing RNA-seq exon counts between samples with different\nexperimental designs. It provides functions that allows the\nuser to make the necessary statistical tests based on a model\nthat uses the negative binomial distribution to estimate the\nvariance between biological replicates and generalized linear\nmodels for testing. The package also provides functions for the\nvisualization and exploration of the results.",
  "License": "GPL (>= 3)",
  "URL": "",
  "biocViews": "ImmunoOncology, Sequencing, RNASeq, DifferentialExpression,\nAlternativeSplicing, DifferentialSplicing, GeneExpression,\nVisualization",
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  "Encoding": "UTF-8",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:31 UTC",
  "RemoteUrl": "https://github.com/bioc/DEXSeq",
  "RemoteRef": "HEAD",
  "RemoteSha": "93934728c6c0712dad770aed93c897cc8aff2ac2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:45:35 UTC",
    "User": "root"
  },
  "Author": "Simon Anders [aut],\nAlejandro Reyes [aut, ccp] (Maintainer until 2026.),\nHugo Gruson [cre]",
  "Maintainer": "Hugo Gruson <hugo.gruson@embl.de>",
  "MD5sum": "3658d384db83eb376ec5f42a07b676a7",
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    "mastodon": "@grusonh@mastodon.social",
    "description": "Evolutionary Biologist turned Research Software Engineer in R.",
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    "immunooncology",
    "sequencing",
    "rnaseq",
    "differentialexpression",
    "alternativesplicing",
    "differentialsplicing",
    "geneexpression",
    "visualization"
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "extra/citation.json",
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    "manual.pdf"
  ],
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  "_exports": [
    "colData<-",
    "counts",
    "DEXSeq",
    "DEXSeqDataSet",
    "DEXSeqDataSetFromHTSeq",
    "DEXSeqDataSetFromSE",
    "DEXSeqHTML",
    "DEXSeqResults",
    "estimateDispersions",
    "estimateExonFoldChanges",
    "estimateSizeFactors",
    "exonIDs",
    "exonIDs<-",
    "featureCounts",
    "featureIDs",
    "featureIDs<-",
    "findOverlaps",
    "geneIDs",
    "geneIDs<-",
    "groupIDs",
    "groupIDs<-",
    "perGeneQValue",
    "plotDEXSeq",
    "plotMA",
    "sampleAnnotation",
    "subsetByOverlaps",
    "testForDEU"
  ],
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    {
      "page": "counts",
      "title": "Accessors for the 'counts' slot of a DEXSeqResults object.",
      "topics": [
        "counts",
        "counts,DEXSeqResults-method"
      ]
    },
    {
      "page": "DEXSeq",
      "title": "Performs the differential exon usage test in a single command",
      "topics": [
        "DEXSeq"
      ]
    },
    {
      "page": "DEXSeq-defunct",
      "title": "This functions are deprecated and will become defunct.",
      "topics": [
        "DEXSeq-defunct"
      ]
    },
    {
      "page": "DEXSeqDataSet",
      "title": "DEXSeqDataSet object and constructors",
      "topics": [
        "DEXSeqDataSet",
        "DEXSeqDataSet-class",
        "DEXSeqDataSetFromHTSeq",
        "DEXSeqDataSetFromSE"
      ]
    },
    {
      "page": "otherMethods",
      "title": "Subset and replacements of DEXSeqDataSet slots",
      "topics": [
        "$<-,DEXSeqDataSet-method",
        "colData<-,DEXSeqDataSet,DataFrame-method",
        "[,DEXSeqDataSet,ANY,ANY,ANY-method",
        "[,DEXSeqDataSet,ANY,ANY-method",
        "[,DEXSeqDataSet,ANY-method",
        "[,DEXSeqDataSet-method"
      ]
    },
    {
      "page": "DEXSeqHTML",
      "title": "DEXSeq HTML report writer",
      "topics": [
        "DEXSeqHTML"
      ]
    },
    {
      "page": "DEXSeqResults",
      "title": "DEXSeqResults object",
      "topics": [
        "DEXSeqResults",
        "DEXSeqResults-class"
      ]
    },
    {
      "page": "estimateDispersions",
      "title": "Estimate the dispersions for a DEXSeqDataSet",
      "topics": [
        "estimateDispersions",
        "estimateDispersions,DEXSeqDataSet-method"
      ]
    },
    {
      "page": "estimateExonFoldChanges",
      "title": "Estimates exon usage coefficients from the fitted terms of the GLM.",
      "topics": [
        "estimateExonFoldChanges"
      ]
    },
    {
      "page": "estimateSizeFactors",
      "title": "Estimate the size factors for a DEXSeqDataSet",
      "topics": [
        "estimateSizeFactors",
        "estimateSizeFactors,DEXSeqDataSet-method"
      ]
    },
    {
      "page": "accessors",
      "title": "Accessor functions for DEXSeqDataSet details",
      "topics": [
        "exonIDs",
        "exonIDs<-",
        "featureCounts",
        "featureIDs",
        "featureIDs<-",
        "geneIDs",
        "geneIDs<-",
        "groupIDs",
        "groupIDs<-",
        "sampleAnnotation"
      ]
    },
    {
      "page": "methods-gr",
      "title": "Methods from GRanges overlaps for the DEXSeq object",
      "topics": [
        "findOverlaps",
        "findOverlaps,DEXSeqResults,GenomicRanges-method",
        "findOverlaps-methods",
        "subsetByOverlaps",
        "subsetByOverlaps,DEXSeqResults,GenomicRanges-method",
        "subsetByOverlaps-methods"
      ]
    },
    {
      "page": "perGeneQValue",
      "title": "Summarize per-exon p-values into per-gene q-values.",
      "topics": [
        "perGeneQValue"
      ]
    },
    {
      "page": "plotDEXSeq",
      "title": "Visualization of the per gene DEXSeq results.",
      "topics": [
        "plotDEXSeq"
      ]
    },
    {
      "page": "plotDispEsts",
      "title": "Plot dispersion estimates",
      "topics": [
        "plotDispEsts",
        "plotDispEsts,DEXSeqDataSet-method"
      ]
    },
    {
      "page": "plotMA",
      "title": "Generate an MA plot",
      "topics": [
        "plotMA",
        "plotMA,DEXSeqDataSet-method",
        "plotMA,DEXSeqResults-method",
        "plotMA-methods"
      ]
    },
    {
      "page": "testForDEU",
      "title": "Test for Differential Exon Usage",
      "topics": [
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      ]
    }
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      "source": "DEXSeq.Rmd",
      "filename": "DEXSeq.html",
      "title": "Inferring differential exon usage in RNA-Seq data with the DEXSeq package",
      "author": "Alejandro Reyes, Simon Anders, Wolfgang Huber",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Preparations",
        "Example data",
        "Executability of the code",
        "Alignment",
        "Preparing the annotation",
        "Counting reads",
        "Building a DEXSeqDataSet",
        "Standard analysis workflow",
        "Loading and inspecting the example data",
        "Normalisation",
        "Dispersion estimation",
        "Testing for differential exon usage",
        "Additional technical or experimental variables",
        "Visualization",
        "Parallelization and large number of samples",
        "Perform a standard differential exon usage analysis in one command",
        "Appendix",
        "Controlling FDR at the gene level",
        "Preprocessing with python",
        "Preparing the annotation file with python",
        "Counting reads with python",
        "Reading the data from the python ouputs into R",
        "Preprocessing using featureCounts",
        "Further accessors",
        "Overlap operations",
        "Methodological changes since publication of the paper",
        "Requirements on GTF files",
        "Session Information",
        "References"
      ],
      "created": "2019-03-01 02:36:10",
      "modified": "2026-04-08 07:51:23",
      "commits": 11
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