Introduction | High-level workflow | Installation | Quick Start | What is Entropy and Tsallis Entropy? | Historical Foundation and Intellectual Progression | Why This Matters for RNA-seq: The Isoform Complexity Problem | Mathematical Foundation and Interpretation | Tsallis Entropy: Definition and Intuition | The q Parameter: A Sensitivity Dial for Distribution Scales | 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 | Configuring the Switching Analysis | Key Interpretation Questions | Delta Influence Across Diversity Scales | Effect Size Analysis | Interpretation of Pattern Types: | Appendices | References | Session Information

Introduction | Two Complementary Approaches | Why Two Methods for One Question? | Setup | Computing Tsallis Entropy with Pseudocount Regularization | Aligned Rank Transform (ART) | Assumption Validation | Running the ART Analysis | Generalized Additive Mixed Model Approach (GAMM) | Method Concordance Analysis | Statistical Power vs. Robustness: Understanding Method Discordance | Visualization: Method Comparison | Session Information

Introduction | 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: Endpoint Equivalence Summary | Session Information