BenchmarkIntegration    Benchmark integration quality with
                        scIB-inspired metrics
CreateBacObject         Create a standardized bacterial single-cell
                        object
FilterBacCells          Filter cells using bacterial QC thresholds
IntegrateBacData        Integrate microbial single-cell batches
MergeBacObjects         Merge multiple scProkaR or SingleCellExperiment
                        objects
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
RunBacQC                Compute bacterial QC metrics
RunIntegratedClustering
                        Cluster cells on an integrated embedding
RunIntegratedUMAP       Run UMAP on an existing embedding
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
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
directed_reachability_concordance
                        Quantify how well a directed cluster graph
                        follows real time
filter_pseudobulk_samples
                        Filter pseudobulk samples by size
local_temporal_order_metrics
                        Compute local temporal order metrics on a cell
                        graph
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
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
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
