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  "Title": "circRNAprofiler: An R-Based Computational Framework for the\nDownstream Analysis of Circular RNAs",
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  "Description": "R-based computational framework for a comprehensive in\nsilico analysis of circRNAs. This computational framework\nallows to combine and analyze circRNAs previously detected by\nmultiple publicly available annotation-based circRNA detection\ntools. It covers different aspects of circRNAs analysis from\ndifferential expression analysis, evolutionary conservation,\nbiogenesis to functional analysis.",
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      "title": "Screen target sequences for recurrent motifs",
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      "title": "Retrieve random back-spliced junctions",
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    {
      "page": "getRegexPattern",
      "title": "Convert IUPAC sequence to an regular expression",
      "topics": [
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    {
      "page": "getSeqsAcrossBSJs",
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      "title": "Plot exons between back-spliced junctions",
      "topics": [
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    {
      "page": "plotExPosition",
      "title": "Plot back-spliced exon positions",
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    {
      "page": "plotHostGenes",
      "title": "Plot circRNA host genes",
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    {
      "page": "plotLenBSEs",
      "title": "Plot length back-spliced exons",
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      "page": "plotLenIntrons",
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      "page": "plotMiR",
      "title": "Plot miRNA analysis results",
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      "page": "plotMotifs",
      "title": "Plot motifs analysis results",
      "topics": [
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      "page": "plotTotExons",
      "title": "Plot exons in the circRNA host transcript",
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      "page": "rearrangeMiRres",
      "title": "Rearrange miR results",
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      "page": "volcanoPlot",
      "title": "Plot differential circRNA expression results",
      "topics": [
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  "_vignettes": [
    {
      "source": "circRNAprofiler.Rmd",
      "filename": "circRNAprofiler.html",
      "title": "circRNAprofiler: An R-based computational framework for the downstream analysis of circular RNAs",
      "author": "Simona Aufiero",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Table of Contents",
        "Introduction",
        "Install the package",
        "Load the package",
        "Running circRNAprofiler",
        "Module 1 - Set up project folder",
        "initCircRNAprofiler()",
        "checkProjectFolder()",
        "Module 2 - Import predicted circRNAs",
        "formatGTF()",
        "getBackSplicedJunctions()",
        "Module 3 - Merge commonly identified circRNAs",
        "mergeBSJunctions()",
        "Module 4 - Filter circRNAs",
        "filterCirc()",
        "Module 5 - Find differentially expressed circRNAs",
        "getDeseqRes()",
        "getEdgerRes()",
        "Module 6 - Map BSJ coordinates between species and genome assemblies",
        "liftBSJcoords()",
        "Module 7 - Annotate circRNAs internal structure and flanking introns",
        "annotateBSJs()",
        "Module 8 - Generate random BSJs",
        "getRandomBSJunctions()",
        "Retrieve target sequences",
        "Module 9 - Retrieve internal circRNA sequences",
        "getCircSeqs()",
        "Module 10 - Retrieve BSJ sequences",
        "getSeqsAcrossBSJs()",
        "Module 11 - Retrieve sequences flanking the BSJs",
        "getSeqsFromGRs()",
        "Screen target sequences",
        "Module 12 - Screen target sequences for RBP/de Novo motifs",
        "getMotifs()",
        "mergeMotifs()",
        "Module 13 - Screen circRNA sequences for miRNA binding sites",
        "getMiRsites()",
        "rearrageMiRres()",
        "Annotate target sequences",
        "Module 14 - Annotate GWAS SNPs",
        "annotateSNPsGWAS()",
        "Module 15 - Annotate repetitive elements",
        "annotateRepeats()",
        "Support",
        "Citation",
        "Acknowledgement",
        "Note",
        "References"
      ],
      "created": "2019-05-10 09:49:22",
      "modified": "2023-10-13 11:45:35",
      "commits": 52
    }
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  "_indexed": true,
  "_nocasepkg": "circrnaprofiler",
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    "aufiero"
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