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_concordance   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
filter_analysis         Filter Low-Abundance Transcripts in a
                        TSENATAnalysis Object
metadata,TSENATAnalysis-method
                        Metadata Accessor Methods
plot_concordance        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
TSENAT                  Run complete TSENAT analysis pipeline
TSENAT_config           Create and return TSENAT configuration
TSENATAnalysis          Constructor for TSENATAnalysis objects
TSENATAnalysis-class    TSENATAnalysis S4 Class Definition
