Package index • TSENAT

All functions

AllGenerics: Generic Functions for TSENATAnalysis S4 Class
TSENAT(): Run complete TSENAT analysis pipeline
`[`(<TSENATAnalysis>,<ANY>,<ANY>,<ANY>): TSENATAnalysis S4 Class Definition
se(): Extract SummarizedExperiment from TSENATAnalysis
TSENATAnalysis(): Constructor for TSENATAnalysis objects
TSENAT_config(): Create and return TSENAT configuration
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_lm(): Calculate LM interactions and store in TSENATAnalysis
calculate_m_estimator(): M-Estimation for Sample Quality (S4 Wrapper)
calculate_srh(): Detect q-dependent gene interactions
filter_analysis(): Filter Low-Abundance Transcripts in a TSENATAnalysis Object
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_lm(): Plot GAM q-curves from TSENATAnalysis object
readcounts: Example transcript-level read counts dataset
results(): Extract analysis results from TSENATAnalysis object