# TSENAT 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.
