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  "Title": "Create, manipulate, visualize splicing graphs, and assign\nRNA-seq reads to them",
  "Description": "This package allows the user to create, manipulate, and\nvisualize splicing graphs and their bubbles based on a gene\nmodel for a given organism. Additionally it allows the user to\nassign RNA-seq reads to the edges of a set of splicing graphs,\nand to summarize them in different ways.",
  "biocViews": "Genetics, Annotation, DataRepresentation, Visualization,\nSequencing, RNASeq, GeneExpression, AlternativeSplicing,\nTranscription, ImmunoOncology",
  "URL": "https://bioconductor.org/packages/SplicingGraphs",
  "BugReports": "https://github.com/Bioconductor/SplicingGraphs/issues",
  "Version": "1.52.0",
  "License": "Artistic-2.0",
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  "Author": "D. Bindreither, M. Carlson, M. Morgan, H. Pagès",
  "Maintainer": "H. Pagès <hpages.on.github@gmail.com>",
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  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:37:41 UTC",
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  "_created": "2026-11-01T18:54:57.000Z",
  "_published": "2026-11-01T23:38:38.241Z",
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    "sgedgesByTranscript",
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    "sgraph",
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    "show",
    "slideshow",
    "SplicingGraphs",
    "strand",
    "toy_genes_gff",
    "toy_overlaps",
    "toy_reads_bam",
    "toy_reads_sam",
    "txpath",
    "txweight",
    "txweight<-",
    "uninformativeSSids",
    "updateObject"
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      "title": "Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them",
      "topics": [
        "SplicingGraphs-package"
      ]
    },
    {
      "page": "assignReads",
      "title": "Assign reads to the edges of a SplicingGraphs object",
      "topics": [
        "assignReads",
        "removeReads"
      ]
    },
    {
      "page": "bubbles-methods",
      "title": "Compute the bubbles of a splicing graph",
      "topics": [
        "ASCODE2DESC",
        "bubbles",
        "bubbles,ANY-method",
        "bubbles,IntegerList-method",
        "bubbles,SplicingGraphs-method",
        "bubbles-methods"
      ]
    },
    {
      "page": "countReads-methods",
      "title": "Summarize the reads assigned to a SplicingGraphs object",
      "topics": [
        "countReads",
        "countReads,SplicingGraphs-method",
        "countReads-methods"
      ]
    },
    {
      "page": "plotTranscripts-methods",
      "title": "Plot a set of transcripts along genomic coordinates.",
      "topics": [
        "plotTranscripts",
        "plotTranscripts,GRangesList-method",
        "plotTranscripts,SplicingGraphs-method",
        "plotTranscripts,TxDb-method",
        "plotTranscripts-methods"
      ]
    },
    {
      "page": "rsgedgesByGene-methods",
      "title": "Extract the reduced edges and their ranges from a SplicingGraphs object",
      "topics": [
        "rsgedges",
        "rsgedgesByGene",
        "rsgedgesByGene,SplicingGraphs-method",
        "rsgedgesByGene-methods",
        "rsgedgesByTranscript",
        "rsgedgesByTranscript,SplicingGraphs-method",
        "rsgraph",
        "sgedges2",
        "sgraph2",
        "uninformativeSSids",
        "uninformativeSSids,ANY-method",
        "uninformativeSSids,DataFrame-method"
      ]
    },
    {
      "page": "sgedges-methods",
      "title": "Extract the edges (and nodes) of a splicing graph",
      "topics": [
        "indeg",
        "indeg,ANY-method",
        "indeg,DataFrame-method",
        "outdeg",
        "outdeg,ANY-method",
        "outdeg,DataFrame-method",
        "sgedges",
        "sgedges,SplicingGraphs-method",
        "sgedges-methods",
        "sgnodes",
        "sgnodes,data.frame-method",
        "sgnodes,DataFrame-method",
        "sgnodes,IntegerList-method",
        "sgnodes,SplicingGraphs-method"
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    },
    {
      "page": "sgedgesByGene-methods",
      "title": "Extract the edges and their ranges from a SplicingGraphs object",
      "topics": [
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        "sgedgesByGene",
        "sgedgesByGene,SplicingGraphs-method",
        "sgedgesByGene-methods",
        "sgedgesByTranscript",
        "sgedgesByTranscript,SplicingGraphs-method"
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    },
    {
      "page": "sgraph-methods",
      "title": "Extract a splicing graph as a plottable graph-like object",
      "topics": [
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        "sgraph",
        "sgraph,ANY-method",
        "sgraph,data.frame-method",
        "sgraph,DataFrame-method",
        "sgraph,igraph-method",
        "sgraph-methods",
        "slideshow"
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      "title": "SplicingGraphs objects",
      "topics": [
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        "class:SplicingGraphs",
        "elementNROWS,SplicingGraphs-method",
        "GeneModel-class",
        "isCircular<-,GeneModel-method",
        "isCircular<-,SplicingGraphs-method",
        "length,SplicingGraphs-method",
        "lengths,SplicingGraphs-method",
        "names,SplicingGraphs-method",
        "seqinfo,GeneModel-method",
        "seqinfo,SplicingGraphs-method",
        "seqnames,GeneModel-method",
        "seqnames,SplicingGraphs-method",
        "show,SplicingGraphs-method",
        "SplicingGraphs",
        "SplicingGraphs,GRangesList-method",
        "SplicingGraphs,TxDb-method",
        "SplicingGraphs-class",
        "strand,GeneModel-method",
        "strand,SplicingGraphs-method",
        "unlist,SplicingGraphs-method",
        "updateObject,SplicingGraphs-method",
        "[,SplicingGraphs,ANY,ANY,ANY-method",
        "[[,SplicingGraphs,ANY,ANY-method"
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    },
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        "toy_overlaps",
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        "toy_reads_sam"
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    {
      "page": "TSPCsg",
      "title": "TSPC splicing graphs",
      "topics": [
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        "TSPCsg"
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      "title": "Extract the transcript paths of a splicing graph",
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        "txpath,GRangesList-method",
        "txpath,SplicingGraphs-method",
        "txpath-methods",
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        "txweight,SplicingGraphs-method",
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