# Tsallis Entropy Analysis Toolbox

## Documentation for package ‘TSENAT’ version 0.99.23

- 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