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      "title": "Generic Functions for TSENATAnalysis S4 Class",
      "topics": [
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      "title": "Build a Complete TSENATAnalysis Object",
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      "title": "Test statistical assumptions on diversity data in TSENATAnalysis",
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    {
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      "title": "Calculate divergence metrics and store in TSENATAnalysis",
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    {
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      "title": "Calculate diversity and store in TSENATAnalysis",
      "topics": [
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      "title": "Compute Effect Sizes from Divergence Results (S4 Wrapper)",
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      "title": "M-Estimation for Sample Quality (S4 Wrapper)",
      "topics": [
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      "topics": [
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    {
      "page": "calculate_sait",
      "title": "Calculate SAIT interactions and store in TSENATAnalysis",
      "topics": [
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    {
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      "title": "Filter Low-Abundance Transcripts in a TSENATAnalysis Object",
      "topics": [
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      "title": "Metadata Accessor Methods",
      "topics": [
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        "metadata<-,TSENATAnalysis-method"
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    {
      "page": "plot_concordance",
      "title": "Plot method concordance results from TSENATAnalysis",
      "topics": [
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        "plot_concordance,TSENATAnalysis-method"
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    },
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      "page": "plot_divergence_distribution",
      "title": "Plot Tsallis Divergence Effect Size Distribution (S4 Wrapper)",
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    },
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      "page": "plot_divergence_spectrum",
      "title": "Plot Global Divergence q-Curve Across All Genes (S4 Wrapper)",
      "topics": [
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    },
    {
      "page": "plot_diversity_spectrum",
      "title": "Plot Tsallis Entropy q-Curve",
      "topics": [
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    {
      "page": "plot_diversity_violin_density",
      "title": "Combined Violin and Density Plot Grid for Single q Value",
      "topics": [
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      "title": "Plot Top Transcripts from TSENATAnalysis Object",
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      "title": "Plot Multi-Q Delta Influence Heatmaps from TSENATAnalysis Object",
      "topics": [
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    {
      "page": "plot_sait",
      "title": "Plot GAM q-curves from TSENATAnalysis object",
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      "page": "readcounts",
      "title": "Example transcript-level read counts dataset",
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        "Introduction",
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        "What is Entropy and Tsallis Entropy?",
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        "Why This Matters for RNA-seq: The Isoform Complexity Problem",
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        "Benchmark Results Summary",
        "Shannon Entropy (SplicingFactory Laplace vs TSENAT Tsallis q=1)",
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