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Changelog

Source: NEWS.md

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_lm() for linear models/GAM interaction analysis, 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.