Tsallis Entropy Analysis Toolbox

---

Documentation for package ‘TSENAT’ version 0.99.17

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

AllGenerics	Generic Functions for TSENATAnalysis S4 Class
build_analysis	Build a Complete TSENATAnalysis Object
calculate_assumptions	Test statistical assumptions on diversity data in TSENATAnalysis
calculate_assumptions-method	Test statistical assumptions on diversity data in TSENATAnalysis
calculate_concordance	Compare method concordance for differential analysis results
calculate_concordance-method	Compare method concordance for differential analysis results
calculate_divergence	Calculate divergence metrics and store in TSENATAnalysis
calculate_diversity	Calculate diversity and store in TSENATAnalysis
calculate_effect_sizes	Compute Effect Sizes from Divergence Results (S4 Wrapper)
calculate_jeo	Jackknife resampling with confidence intervals
calculate_jis	Jackknife isoform switching analysis on TSENATAnalysis object
calculate_m_estimator	M-Estimation for Sample Quality (S4 Wrapper)
calculate_sait	Calculate SAIT interactions and store in TSENATAnalysis
calculate_srh	Detect q-dependent gene interactions
effective_length	Example transcript-level read counts dataset
filter_analysis	Filter Low-Abundance Transcripts in a TSENATAnalysis Object
metadata-method	Metadata Accessor Methods
metadata<--method	Metadata Accessor Methods
plot_concordance	Plot method concordance results from TSENATAnalysis
plot_concordance-method	Plot method concordance results from TSENATAnalysis
plot_divergence_distribution	Plot Tsallis Divergence Effect Size Distribution (S4 Wrapper)
plot_divergence_spectrum	Plot Global Divergence q-Curve Across All Genes (S4 Wrapper)
plot_diversity_spectrum	Plot Tsallis Entropy q-Curve
plot_diversity_violin_density	Combined Violin and Density Plot Grid for Single q Value
plot_expression	Plot Top Transcripts from TSENATAnalysis Object
plot_jis_delta	Plot Multi-Q Delta Influence Heatmaps from TSENATAnalysis Object
plot_sait	Plot GAM q-curves from TSENATAnalysis object
readcounts	Example transcript-level read counts dataset
results	Extract analysis results from TSENATAnalysis object
se	Extract SummarizedExperiment from TSENATAnalysis
se-method	Extract SummarizedExperiment from TSENATAnalysis
tpm	Example transcript-level read counts dataset
TSENAT	Run complete TSENAT analysis pipeline
TSENATAnalysis	Constructor for TSENATAnalysis objects
TSENATAnalysis-class	TSENATAnalysis S4 Class Definition
TSENAT_config	Create and return TSENAT configuration
[-method	TSENATAnalysis S4 Class Definition