Package index
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build_se() - Build a SummarizedExperiment from transcript readcounts and tx->gene map
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calculate_difference() - Calculate splicing diversity changes between two conditions.
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calculate_diversity() - Calculate Tsallis diversity per gene across samples
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calculate_fc() - Calculate splicing diversity changes between two conditions.
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calculate_lm_interaction() - Linear-model interaction test for Tsallis entropy For each gene, fit a linear model of the form `entropy ~ q * group` and extract the p-value for the interaction term (whether the effect of `q` differs between groups). The function expects a `SummarizedExperiment` produced by `calculate_diversity()` when multiple `q` values have been computed (column names contain `_q=`).
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calculate_method() - Calculate Tsallis diversity values for transcripts grouped by gene
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calculate_tsallis_entropy() - Calculate Tsallis entropy for a vector of transcript-level expression values of one gene.
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extract_tx2gene_from_gff3() - Extract Transcript-to-Gene Mapping from GFF3 File
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filter_se() - Filter transcripts in a `SummarizedExperiment` by minimum count/sample
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label_shuffling() - Calculate p-values using label shuffling.
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map_metadata() - Map external coldata into a SummarizedExperiment
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map_tx_to_readcounts() - Map transcript IDs from a tx2gene table to a readcounts matrix
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plot_diversity_density() - Plot diversity distributions (density) by sample type
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plot_ma_expression() - Plot MA using expression/readcount-based fold changes
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plot_ma_tsallis() - Plot MA using Tsallis-based fold changes
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plot_mean_violin() - Plot violin of per-gene mean diversity by sample type
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plot_top_transcripts() - Plot top transcripts for a gene
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plot_tsallis_density_multq() - Density plot of Tsallis entropy for multiple q values
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plot_tsallis_gene_profile() - Plot q-curve profile for a single gene comparing groups
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plot_tsallis_q_curve() - Plot median +- IQR of Tsallis entropy across q values by group
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plot_tsallis_violin_multq() - Violin plot of Tsallis entropy for multiple q values
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plot_volcano() - Volcano plot for differential results
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tcga_brca_luma - TCGA Luminal A breast cancer dataset (transcript-level)
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test_differential() - Run a differential test by name: Wilcoxon or label-shuffle
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wilcoxon() - Calculate p-values using Wilcoxon rank sum test.