Package: TSENAT 0.99.35

Cristóbal Gallardo Alba

TSENAT: Tsallis Entropy Analysis Toolbox

Quantifies and models isoform-usage complexity in RNA-seq data using Tsallis entropy, a scale-dependent diversity measure. By tuning the entropic index parameter (q), TSENAT examines transcriptome heterogeneity at different scales: rare variants (low q) or dominant isoforms (high q). It enables computing Tsallis entropy and Tsallis divergence from transcript-level estimates, comparing measures between conditions, testing for differences, and visualizing scale-dependent complexity via q-curves.

Authors:Cristóbal Gallardo Alba [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TSENAT/json (API)

# Install 'TSENAT' in R:
install.packages('TSENAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gallardoalba/tsenat/issues

Pkgdown/docs site:https://gallardoalba.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • effective_length - Example transcript-level read counts dataset
  • readcounts - Example transcript-level read counts dataset
  • tpm - Example transcript-level read counts dataset

On BioConductor:TSENAT-0.99.35(bioc 3.24)

transcriptomicsrnaseqdifferentialsplicingalternativesplicingtranscriptomevariantgeneexpressiondifferentialexpressioncomplex-systemsisoform-diversityrna-seqtsallis-entropycpp

6.13 score 2 stars 28 scripts 301 downloads 27 exports 110 dependencies

Last updated from:f7238211a4. Checks:14 NOTE, 2 OK. Indexed: yes.

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Exports:build_analysiscalculate_assumptionscalculate_concordancecalculate_divergencecalculate_diversitycalculate_effect_sizescalculate_jeocalculate_jiscalculate_m_estimatorcalculate_rank_transformcalculate_saitfilter_analysismetadatametadata<-plot_concordanceplot_divergence_distributionplot_divergence_spectrumplot_diversity_spectrumplot_diversity_violin_densityplot_expressionplot_jis_deltaplot_saitresultsseTSENATTSENAT_configTSENATAnalysis

Dependencies:abindARToolbackportsBHBiobaseBiocGenericsBiocParallelbitbit64bootbroomcachemcarcarDataclicliprcodetoolscolorspacecowplotcpp11crayonDelayedArrayDerivdigestdoBydplyremmeansestimabilityfarverfastmapforecastformatRFormulafracdifffutile.loggerfutile.optionsgeepackgenericsGenomicRangesggplot2gluegtablehmsIRangesisobandlabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvminqamodelrmvtnormnlmenloptrnnetnumDerivpbkrtestpheatmappillarpkgconfigplyrprettyunitsprogresspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasrlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDatetzdburcautf8vctrsviridisLitevroomwithrXVectorzoo

TSENAT: Tsallis Entropy Analysis Toolbox
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
Rendered fromTSENAT.Rmdusingknitr::rmarkdown

Last update: 2026-08-17
Started: 2026-01-31

Appendix B: Cross-Method Robustness and Concordance of Scale-Adaptive Interaction Test Results via GAMM and Aligned Rank Transform (ART)
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
Rendered fromTSENAT_appendix_B.Rmdusingknitr::rmarkdown

Last update: 2026-08-17
Started: 2026-04-06

Appendix A: Endpoint Equivalence with SplicingFactory
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
Rendered fromTSENAT_appendix_A.Rmdusingknitr::rmarkdown

Last update: 2026-08-17
Started: 2026-04-06

Readme and manuals

Help Manual

Help pageTopics
Generic Functions for TSENATAnalysis S4 ClassAllGenerics
Build a Complete TSENATAnalysis Objectbuild_analysis
Test statistical assumptions on diversity data in TSENATAnalysiscalculate_assumptions calculate_assumptions,TSENATAnalysis-method
Compare method concordance for differential analysis resultscalculate_concordance calculate_concordance,TSENATAnalysis-method
Calculate divergence metrics and store in TSENATAnalysiscalculate_divergence
Calculate diversity and store in TSENATAnalysiscalculate_diversity
Compute Effect Sizes from Divergence Results (S4 Wrapper)calculate_effect_sizes
Jackknife resampling with confidence intervalscalculate_jeo
Jackknife isoform switching analysis on TSENATAnalysis objectcalculate_jis
M-Estimation for Sample Quality (S4 Wrapper)calculate_m_estimator
Detect q-dependent gene interactionscalculate_rank_transform
Calculate SAIT interactions and store in TSENATAnalysiscalculate_sait
Filter Low-Abundance Transcripts in a TSENATAnalysis Objectfilter_analysis
Metadata Accessor Methodsmetadata,TSENATAnalysis-method metadata<-,TSENATAnalysis-method
Plot method concordance results from TSENATAnalysisplot_concordance plot_concordance,TSENATAnalysis-method
Plot Tsallis Divergence Effect Size Distribution (S4 Wrapper)plot_divergence_distribution
Plot Global Divergence q-Curve Across All Genes (S4 Wrapper)plot_divergence_spectrum
Plot Tsallis Entropy q-Curveplot_diversity_spectrum
Combined Violin and Density Plot Grid for Single q Valueplot_diversity_violin_density
Plot Top Transcripts from TSENATAnalysis Objectplot_expression
Plot Multi-Q Delta Influence Heatmaps from TSENATAnalysis Objectplot_jis_delta
Plot GAM q-curves from TSENATAnalysis objectplot_sait
Example transcript-level read counts dataseteffective_length readcounts tpm
Extract analysis results from TSENATAnalysis objectresults
Extract SummarizedExperiment from TSENATAnalysisse se,TSENATAnalysis-method
Run complete TSENAT analysis pipelineTSENAT
Create and return TSENAT configurationTSENAT_config
Constructor for TSENATAnalysis objectsTSENATAnalysis
TSENATAnalysis S4 Class DefinitionTSENATAnalysis-class [,TSENATAnalysis,ANY,ANY,ANY-method