{
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  "Package": "rnaseqDTU",
  "Title": "RNA-seq workflow for differential transcript usage following\nSalmon quantification",
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  "Date": "2018-06-27",
  "Authors@R": "c(person(role=c(\"aut\", \"cre\"), \"Michael\", \"Love\", email = \"michaelisaiahlove@gmail.com\"),\nperson(role=c(\"aut\"), \"Charlotte\", \"Soneson\"),\nperson(role=c(\"aut\"), \"Rob\", \"Patro\"))",
  "Description": "RNA-seq workflow for differential transcript usage (DTU)\nfollowing Salmon quantification. This workflow uses\nBioconductor packages tximport, DRIMSeq, and DEXSeq to perform\na DTU analysis on simulated data. It also shows how to use\nstageR to perform two-stage testing of DTU, a statistical\nframework to screen at the gene level and then confirm which\ntranscripts within the significant genes show evidence of DTU.",
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  "Date/Publication": "2026-04-28 12:43:26 UTC",
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      "source": "rnaseqDTU.Rmd",
      "filename": "rnaseqDTU.html",
      "title": "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification",
      "author": "Michael I. Love, Charlotte Soneson, Rob Patro",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Getting help",
        "Introduction",
        "Methods",
        "Simulation",
        "Operation",
        "Quantification and data import",
        "DTU testing",
        "Workflow",
        "Salmon quantification",
        "Importing counts into R/Bioconductor",
        "Transcript-to-gene mapping",
        "Statistical analysis of differential transcript usage",
        "DRIMSeq",
        "stageR following DRIMSeq",
        "Post-hoc filtering on the standard deviation in proportions",
        "DEXSeq",
        "stageR following DEXSeq",
        "Citing methods in published research",
        "DTU analysis complements DGE analysis",
        "DGE analysis with DESeq2",
        "DGE analysis with edgeR",
        "End of workflow section",
        "Discussion",
        "Session information",
        "Software versions",
        "Data availability",
        "Acknowledgments",
        "References"
      ],
      "created": "2018-06-05 16:47:12",
      "modified": "2019-07-16 18:31:46",
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