Changes in version 0.99.0                        

  - Initial Bioconductor release. TSENAT provides scale-dependent
    analysis of transcript isoform diversity using Tsallis entropy,
    enabling detection of splicing-driven regulatory changes orthogonal
    to count-based differential expression methods.

  - Core analysis via calculate_diversity(), calculate_divergence(),
    calculate_srh() for Q×Condition interaction testing,
    calculate_sait() for scale-adaptive interaction testing (GAM, LMM,
    GEE, FPCA) with AR(1) support for repeated measures, and
    calculate_concordance() for method comparison. Supports
    Scheirer-Ray-Hare rank-based tests, permutation tests, and jackknife
    bootstrap.

  - Parameter q tunes Tsallis entropy sensitivity: q < 1 emphasizes rare
    isoforms, q ≈ 1 recovers Shannon entropy, q > 1 emphasizes dominant
    isoforms.

  - Unified S4 class TSENATAnalysis integrating SummarizedExperiment,
    configuration, results, and cached plots with full subsetting and
    accessor support.

  - Data input: build_analysis() for RNA-seq count matrices or Salmon
    quantification (via internal utilities); supports GFF3 annotation
    files for transcript-to-gene mapping via tx2gene parameter.

  - Quality control: filter_analysis() for multi-criteria filtering;
    jackknife_entropy_outliers_s4() for outlier detection.

  - Visualization suite (8 plot types): diversity q-curves, volcano/MA
    plots, violin/density plots, transcript composition heatmaps,
    divergence distance matrices, interaction surfaces, concordance
    plots, multi-gene q-spectrum plots. All ggplot2-based with
    publication-ready styling.

  - High-level workflow orchestration via TSENAT() and flexible
    configuration management with TSENAT_config().

  - Performance: Rcpp/RcppArmadillo for entropy calculations,
    BiocParallel support, lazy-loading of visualization libraries (~30%
    faster non-plot workflows).

  - Comprehensive documentation: main vignette + 2 appendices
    (SplicingFactory validation, advanced workflows), 25 exported
    functions with complete roxygen2 documentation.