Package: TSENAT 0.99.24

Cristóbal Gallardo

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 [aut, cre]

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

# 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-0.99.21(bioc 3.24)

transcriptomicsrnaseqdifferentialsplicingalternativesplicingtranscriptomevariantgeneexpressiondifferentialexpressioncomplex-systemsisoform-diversityrna-seqtsallis-entropycpp

5.65 score 27 scripts 27 exports 77 dependencies

Last updated from:114c29e56f. Checks:12 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE244
linux-devel-arm64NOTE788
linux-devel-x86_64NOTE855
source / vignettesOK375
linux-release-arm64NOTE741
linux-release-x86_64NOTE846
macos-release-arm64NOTE717
macos-release-x86_64NOTE1029
macos-oldrel-arm64NOTE641
macos-oldrel-x86_64NOTE971
windows-develNOTE1562
windows-releaseNOTE1463
windows-oldrelNOTE1529
wasm-releaseOK183

Exports:build_analysiscalculate_assumptionscalculate_concordancecalculate_divergencecalculate_diversitycalculate_effect_sizescalculate_jeocalculate_jiscalculate_m_estimatorcalculate_saitcalculate_srhfilter_analysismetadatametadata<-plot_concordanceplot_divergence_distributionplot_divergence_spectrumplot_diversity_spectrumplot_diversity_violin_densityplot_expressionplot_jis_deltaplot_saitresultsseTSENATTSENAT_configTSENATAnalysis

Dependencies:abindbackportsBHBiobaseBiocGenericsBiocParallelbitbit64broomcachemclicliprcodetoolscowplotcpp11crayonDelayedArraydigestdplyrfarverfastmapformatRfutile.loggerfutile.optionsgeepackgenericsGenomicRangesggplot2gluegtablehmsIRangesisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvnlmepheatmappillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrrlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXVector

TSENAT: Tsallis Entropy Analysis Toolbox

Cristobal Gallardo [email protected]

Rendered fromTSENAT.Rmdusingknitr::rmarkdownon Jun 22 2026.

Last update: 2026-05-20
Started: 2026-01-31

Appendix A: Equivalence Validation - TSENAT vs SplicingFactory

Cristobal Gallardo [email protected]

Rendered fromTSENAT_appendix_A.Rmdusingknitr::rmarkdownon Jun 22 2026.

Last update: 2026-05-20
Started: 2026-04-06

Appendix B: Non-Parametric Validation of Scale-Adaptive Interaction Test Results via GAMM and Rank-Based Methods

Cristobal Gallardo [email protected]

Rendered fromTSENAT_appendix_B.Rmdusingknitr::rmarkdownon Jun 22 2026.

Last update: 2026-05-20
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
Calculate SAIT interactions and store in TSENATAnalysiscalculate_sait
Detect q-dependent gene interactionscalculate_srh
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