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.