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  "Version": "2.44.0",
  "License": "Artistic-2.0",
  "Title": "Flexible, isoform-level differential expression analysis",
  "Description": "Tools for statistical analysis of assembled\ntranscriptomes, including flexible differential expression\nanalysis, visualization of transcript structures, and matching\nof assembled transcripts to annotation.",
  "VignetteBuilder": "knitr",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:28 UTC",
  "RemoteUrl": "https://github.com/bioc/ballgown",
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  "Author": "Jack Fu [aut],\nAlyssa C. Frazee [aut, cre],\nLeonardo Collado-Torres [aut],\nAndrew E. Jaffe [aut],\nJeffrey T. Leek [aut, ths]",
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    "plotLatentTranscripts",
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    "sampleNames",
    "seqnames",
    "stattest",
    "structure",
    "subset",
    "texpr",
    "tGene",
    "transcriptIDs",
    "transcriptNames",
    "writeFiles"
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      "title": "Toy ballgown object",
      "object": "bg",
      "file": "bg.rda",
      "class": [
        "ballgown"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "title": "The ballgown package for analysis of transcript assemblies",
      "topics": [
        "ballgown-package",
        "ballgownp"
      ]
    },
    {
      "page": "annotate_assembly",
      "title": "match assembled transcripts to annotated transcripts",
      "topics": [
        "annotate_assembly"
      ]
    },
    {
      "page": "ballgown-class",
      "title": "Ballgown",
      "topics": [
        "Ballgown",
        "ballgown-class"
      ]
    },
    {
      "page": "ballgown-constructor",
      "title": "constructor function for ballgown objects",
      "topics": [
        "ballgown",
        "ballgown-constructor"
      ]
    },
    {
      "page": "ballgownrsem",
      "title": "load RSEM data into a ballgown object",
      "topics": [
        "ballgownrsem"
      ]
    },
    {
      "page": "bg",
      "title": "Toy ballgown object",
      "topics": [
        "bg"
      ]
    },
    {
      "page": "checkAssembledTx",
      "title": "plot annotated and assembled transcripts together",
      "topics": [
        "checkAssembledTx"
      ]
    },
    {
      "page": "clusterTranscripts",
      "title": "group a gene's assembled transcripts into clusters",
      "topics": [
        "clusterTranscripts"
      ]
    },
    {
      "page": "collapseTranscripts",
      "title": "cluster a gene's transcripts and calculate cluster-level expression",
      "topics": [
        "collapseTranscripts"
      ]
    },
    {
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      "title": "determine if one set of GRanges fully contains any of another set of GRanges",
      "topics": [
        "contains"
      ]
    },
    {
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      "title": "extract paths to tablemaker output",
      "topics": [
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        "dirs,ballgown-method"
      ]
    },
    {
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      "title": "extract exon-level expression measurements from ballgown objects",
      "topics": [
        "eexpr",
        "eexpr,ballgown-method"
      ]
    },
    {
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      "title": "extract expression components from ballgown objects",
      "topics": [
        "expr",
        "expr,ballgown-method"
      ]
    },
    {
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      "title": "Replacement method for expr slot in ballgown objects",
      "topics": [
        "expr<-",
        "expr<-,ballgown-method"
      ]
    },
    {
      "page": "exprfilter",
      "title": "subset ballgown objects using an expression filter",
      "topics": [
        "exprfilter"
      ]
    },
    {
      "page": "geneIDs",
      "title": "get gene IDs from a ballgown object",
      "topics": [
        "geneIDs",
        "geneIDs,ballgown-method"
      ]
    },
    {
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      "title": "get gene names from a ballgown object",
      "topics": [
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        "geneNames,ballgown-method"
      ]
    },
    {
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      "title": "extract a specific field of the \"attributes\" column of a data frame created from a GTF/GFF file",
      "topics": [
        "getAttributeField"
      ]
    },
    {
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      "title": "label assembled transcripts with gene names",
      "topics": [
        "getGenes"
      ]
    },
    {
      "page": "gexpr",
      "title": "extract gene-level expression measurements from ballgown objects",
      "topics": [
        "gexpr",
        "gexpr,ballgown-method"
      ]
    },
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      "topics": [
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      "title": "read in gtf file as GRanges object",
      "topics": [
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    {
      "page": "iexpr",
      "title": "extract transcript-level expression measurements from ballgown objects",
      "topics": [
        "iexpr",
        "iexpr,ballgown-method"
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    },
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      "title": "extract the indexes from ballgown objects",
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        "indexes,ballgown-method"
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      "title": "Replace method for indexes slot in ballgown objects",
      "topics": [
        "indexes<-",
        "indexes<-,ballgown-method"
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      "page": "last",
      "title": "get the last element",
      "topics": [
        "last"
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    {
      "page": "mergedDate",
      "title": "extract package version & creation date from ballgown object",
      "topics": [
        "mergedDate",
        "mergedDate,ballgown-method"
      ]
    },
    {
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    },
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        "pData<-,ballgown,ANY-method"
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      "page": "plotLatentTranscripts",
      "title": "cluster assembled transcripts and plot the results",
      "topics": [
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    },
    {
      "page": "plotMeans",
      "title": "visualize transcript abundance by group",
      "topics": [
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      "title": "visualize structure of assembled transcripts",
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        "sampleNames,ballgown-method"
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      "topics": [
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        "seqnames,ballgown-method"
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      "topics": [
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        "structure,ballgown-method"
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        "subset,ballgown-method"
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    {
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      "title": "extract transcript-level expression measurements from ballgown objects",
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        "texpr",
        "texpr,ballgown-method"
      ]
    },
    {
      "page": "tGene",
      "title": "Connect a transcript to its gene",
      "topics": [
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    },
    {
      "page": "transcriptIDs",
      "title": "get numeric transcript IDs from a ballgown object",
      "topics": [
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        "transcriptIDs,ballgown-method"
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    {
      "page": "transcriptNames",
      "title": "get transcript names from a ballgown object",
      "topics": [
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    {
      "page": "writeFiles",
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      "title": "Flexible isoform-level differential expression analysis with Ballgown",
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        "indexes",
        "other slots",
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