adjacent_timepoint_auc
                        Compute adjacent-timepoint AUC for a pseudotime
                        ordering
aggregate_pseudobulk    Aggregate single-cell data into pseudobulk
                        samples
anticausal_edge_mass    Measure the weight of anti-causal edges in a
                        directed graph
BenchmarkIntegration    Benchmark integration quality with
                        scIB-inspired metrics
branch_onset_metrics    Measure branch-emergence timing from pseudotime
build_knn_graph         Build a cell-cell kNN graph
build_tata_graph        Build the TATA cluster graph
cluster_graph_states    Cluster graph-connected cell states
cluster_tata_gene_trends
                        Cluster TATA gene trends by shape
compute_tata_branch_probabilities
                        Compute TATA branch probabilities and entropy
compute_tata_gene_trends
                        Compute branch-specific TATA gene trends
compute_tata_pseudotime
                        Compute TATA pseudotime
compute_time_weights    Compute time consistency for cluster-cluster
                        edges
compute_topology_weights
                        Compute topology-based cluster connectivity
                        weights
CreateBacObject         Create a standardized bacterial single-cell
                        object
directed_reachability_concordance
                        Quantify how well a directed cluster graph
                        follows real time
filter_pseudobulk_samples
                        Filter pseudobulk samples by size
FilterBacCells          Filter cells using bacterial QC thresholds
IntegrateBacData        Integrate microbial single-cell batches
local_temporal_order_metrics
                        Compute local temporal order metrics on a cell
                        graph
MergeBacObjects         Merge multiple scProkaR or SingleCellExperiment
                        objects
normalize_pseudobulk    Normalize pseudobulk samples for exploratory
                        analysis
orient_pseudotime_to_time
                        Orient pseudotime to match increasing real time
plot_pairwise_de_ma     Plot an MA plot for a pairwise edgeR contrast
plot_pairwise_de_volcano
                        Plot a volcano plot for a pairwise edgeR
                        contrast
plot_tata_branch_confusion
                        Plot truth versus inferred TATA branch
                        assignments
plot_tata_branch_probabilities
                        Plot TATA branch probabilities on an embedding
plot_tata_branch_selection
                        Plot selected cells from one TATA branch
plot_tata_cluster_graph
                        Plot the cluster-level TATA graph
plot_tata_edge_causality
                        Plot TATA edge causality diagnostics
plot_tata_gene_trend_heatmap
                        Plot a heatmap of TATA gene trends
plot_tata_gene_trends   Plot fitted TATA gene trends
plot_tata_results       Plot an overview of TATA results
plot_tata_terminal_probabilities
                        Plot branch probabilities for representative
                        cells
plot_tata_time_calibration
                        Plot TATA time calibration
plot_tata_trajectory_embedding
                        Plot TATA trajectories over an embedding
plot_time_series_deg_curves
                        Plot fitted spline expression curves from
                        time-series DE
PlotIntegrationOverview
                        Plot Seurat-style integration result panels
PlotReduction           Plot any stored reduced dimension
RegisterExistingIntegrationEmbeddings
                        Register existing reduced dimensions as
                        integration embeddings
RegisterIntegrationEmbedding
                        Register an external embedding for benchmarking
                        and downstream analysis
run_edger_pairwise_de   Run pairwise pseudobulk differential expression
                        with edgeR
run_edger_spline_de     Run pseudobulk spline or time-series
                        differential expression with edgeR
run_scproka_de          Run a full scProkaR differential expression
                        workflow
run_tata                Run the full TATA workflow
RunBacQC                Compute bacterial QC metrics
RunIntegratedClustering
                        Cluster cells on an integrated embedding
RunIntegratedUMAP       Run UMAP on an existing embedding
sce1                    Example bacterial single-cell dataset
select_tata_branch_cells
                        Select cells from a TATA branch
simulate_tata_multidrug_sce
                        Simulate a multi-drug branching TATA dataset
simulate_tata_sce       Simulate a divergent TATA dataset
simulate_tata_spiral_sce
                        Simulate an extreme spiral-plus-divergent TATA
                        dataset
