# Generated by roxygen2: do not edit by hand

export(BenchmarkIntegration)
export(CreateBacObject)
export(FilterBacCells)
export(IntegrateBacData)
export(MergeBacObjects)
export(PlotIntegrationOverview)
export(PlotReduction)
export(RegisterExistingIntegrationEmbeddings)
export(RegisterIntegrationEmbedding)
export(RunBacQC)
export(RunIntegratedClustering)
export(RunIntegratedUMAP)
export(adjacent_timepoint_auc)
export(aggregate_pseudobulk)
export(anticausal_edge_mass)
export(branch_onset_metrics)
export(build_knn_graph)
export(build_tata_graph)
export(cluster_graph_states)
export(cluster_tata_gene_trends)
export(compute_tata_branch_probabilities)
export(compute_tata_gene_trends)
export(compute_tata_pseudotime)
export(compute_time_weights)
export(compute_topology_weights)
export(directed_reachability_concordance)
export(filter_pseudobulk_samples)
export(local_temporal_order_metrics)
export(normalize_pseudobulk)
export(orient_pseudotime_to_time)
export(plot_pairwise_de_ma)
export(plot_pairwise_de_volcano)
export(plot_tata_branch_confusion)
export(plot_tata_branch_probabilities)
export(plot_tata_branch_selection)
export(plot_tata_cluster_graph)
export(plot_tata_edge_causality)
export(plot_tata_gene_trend_heatmap)
export(plot_tata_gene_trends)
export(plot_tata_results)
export(plot_tata_terminal_probabilities)
export(plot_tata_time_calibration)
export(plot_tata_trajectory_embedding)
export(plot_time_series_deg_curves)
export(run_edger_pairwise_de)
export(run_edger_spline_de)
export(run_scproka_de)
export(run_tata)
export(select_tata_branch_cells)
export(simulate_tata_divergent_sce)
export(simulate_tata_multidrug_sce)
export(simulate_tata_sce)
export(simulate_tata_spiral_sce)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(methods,as)
importFrom(methods,is)
