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  "Title": "Tsallis Entropy Analysis Toolbox",
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  "Description": "Quantifies and models isoform-usage complexity in RNA-seq\ndata using Tsallis entropy, a scale-dependent diversity\nmeasure. By tuning the entropic index parameter (q), TSENAT\nexamines transcriptome heterogeneity at different scales: rare\nvariants (low q) or dominant isoforms (high q). It enables\ncomputing Tsallis entropy and Tsallis divergence from\ntranscript-level estimates, comparing measures between\nconditions, testing for differences, and visualizing\nscale-dependent complexity via q-curves.",
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        "calculate_assumptions,TSENATAnalysis-method"
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        "calculate_concordance,TSENATAnalysis-method"
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      "page": "calculate_divergence",
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    {
      "page": "calculate_diversity",
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    {
      "page": "calculate_jis",
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    {
      "page": "calculate_m_estimator",
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    {
      "page": "calculate_sait",
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      "topics": [
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    {
      "page": "calculate_srh",
      "title": "Detect q-dependent gene interactions",
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      "page": "filter_analysis",
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        "metadata<-,TSENATAnalysis-method"
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      "page": "plot_concordance",
      "title": "Plot method concordance results from TSENATAnalysis",
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      "page": "plot_divergence_spectrum",
      "title": "Plot Global Divergence q-Curve Across All Genes (S4 Wrapper)",
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      "page": "plot_diversity_spectrum",
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      "title": "Extract SummarizedExperiment from TSENATAnalysis",
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      "title": "Constructor for TSENATAnalysis objects",
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        "[,TSENATAnalysis,ANY,ANY,ANY-method"
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        "Biological Interpretation: Richness and Evenness",
        "Why Multi-Scale Entropy Matters: Biological Contexts",
        "Beyond Classical Abundance Measures",
        "Mechanistic Evidence: Disease and Evolution",
        "TSENAT Main Workflow",
        "Load data and metadata",
        "Data preprocessing and filtering",
        "Compute Tsallis Entropy",
        "Quality Control: Sample Influence Assessment",
        "Scale-Adaptive Interaction Tests",
        "Transcript Switching Across Diversity Scales",
        "Two-Stage Analysis Approach",
        "Key Interpretation Questions",
        "Delta Influence Across Diversity Scales",
        "Effect Size Analysis",
        "Interpretation of Pattern Types:",
        "Appendices",
        "References",
        "Session Information"
      ],
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      "title": "Appendix A: Equivalence Validation - TSENAT vs SplicingFactory",
      "author": "Cristobal Gallardo gallardoalba@pm.me",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Document Structure",
        "Background: Transcript Diversity Concepts",
        "Dataset and Methods",
        "Benchmarking",
        "Importing example data",
        "Data filtering and preprocessing",
        "Transcript diversity calculation",
        "Differential analysis",
        "Benchmark Results Summary",
        "Shannon Entropy (SplicingFactory Laplace vs TSENAT Tsallis q=1)",
        "Top 10 Significant Genes - SplicingFactory (Laplace)",
        "Top 10 Significant Genes - TSENAT (Tsallis q=1)",
        "Simpson Index (SplicingFactory vs TSENAT Tsallis q=2)",
        "Top 10 Significant Genes - SplicingFactory (Simpson)",
        "Top 10 Significant Genes - TSENAT (Tsallis q=2)",
        "Analysis: Simpson Index and Tsallis Entropy at q=2",
        "Conclusion: Equivalence Validation Summary",
        "Session Information"
      ],
      "created": "2026-04-06 23:49:02",
      "modified": "2026-05-20 16:48:30",
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      "source": "TSENAT_appendix_B.Rmd",
      "filename": "TSENAT_appendix_B.html",
      "title": "Appendix B: Non-Parametric Validation of Scale-Adaptive Interaction Test Results via GAMM and Rank-Based Methods",
      "author": "Cristobal Gallardo gallardoalba@pm.me",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Two Complementary Validation Approaches",
        "Why Two Methods for One Question?",
        "Setup",
        "Computing Tsallis Entropy with Pseudocount Regularization",
        "Rank-Based Approach (SRH)",
        "Assumption Validation",
        "SRH Test: Testing q x Condition Interactions",
        "Generalized Additive Mixed Model Approach (GAMM)",
        "Method Concordance Analysis",
        "Statistical Power vs. Robustness: Understanding Method Discordance",
        "Visualization: Method Comparison",
        "Session Information"
      ],
      "created": "2026-04-06 23:49:02",
      "modified": "2026-05-20 16:48:30",
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