scProkaR-package	scProkaR-package
adjacent_timepoint_auc	adjacent_timepoint_auc
aggregate_pseudobulk	aggregate_pseudobulk
anticausal_edge_mass	anticausal_edge_mass
BenchmarkIntegration	BenchmarkIntegration
branch_onset_metrics	branch_onset_metrics
build_knn_graph	build_knn_graph
build_tata_graph	build_tata_graph
cluster_graph_states	cluster_graph_states
cluster_tata_gene_trends	cluster_tata_gene_trends
compute_tata_branch_probabilities	compute_tata_branch_probabilities
compute_tata_gene_trends	compute_tata_gene_trends
compute_tata_pseudotime	compute_tata_pseudotime
compute_time_weights	compute_time_weights
compute_topology_weights	compute_topology_weights
CreateBacObject	CreateBacObject
directed_reachability_concordance	directed_reachability_concordance
FilterBacCells	FilterBacCells
filter_pseudobulk_samples	filter_pseudobulk_samples
IntegrateBacData	IntegrateBacData
local_temporal_order_metrics	local_temporal_order_metrics
MergeBacObjects	MergeBacObjects
normalize_pseudobulk	normalize_pseudobulk
orient_pseudotime_to_time	orient_pseudotime_to_time
PlotIntegrationOverview	PlotIntegrationOverview
PlotReduction	PlotReduction
plot_pairwise_de_ma	plot_pairwise_de_ma
plot_pairwise_de_volcano	plot_pairwise_de_volcano
plot_tata_branch_confusion	plot_tata_branch_confusion
plot_tata_branch_probabilities	plot_tata_branch_probabilities
plot_tata_branch_selection	plot_tata_branch_selection
plot_tata_cluster_graph	plot_tata_cluster_graph
plot_tata_edge_causality	plot_tata_edge_causality
plot_tata_gene_trends	plot_tata_gene_trends
plot_tata_gene_trend_heatmap	plot_tata_gene_trend_heatmap
plot_tata_results	plot_tata_results
plot_tata_terminal_probabilities	plot_tata_terminal_probabilities
plot_tata_time_calibration	plot_tata_time_calibration
plot_tata_trajectory_embedding	plot_tata_trajectory_embedding
plot_time_series_deg_curves	plot_time_series_deg_curves
RegisterExistingIntegrationEmbeddings	RegisterExistingIntegrationEmbeddings
RegisterIntegrationEmbedding	RegisterIntegrationEmbedding
RunBacQC	RunBacQC
RunIntegratedClustering	RunIntegratedClustering
RunIntegratedUMAP	RunIntegratedUMAP
run_edger_pairwise_de	run_edger_pairwise_de
run_edger_spline_de	run_edger_spline_de
run_scproka_de	run_scproka_de
run_tata	run_tata
sce1	sce1
scProkaR	scProkaR-package
select_tata_branch_cells	select_tata_branch_cells
simulate_tata_divergent_sce	simulate_tata_sce
simulate_tata_multidrug_sce	simulate_tata_multidrug_sce
simulate_tata_sce	simulate_tata_sce
simulate_tata_spiral_sce	simulate_tata_spiral_sce
