Microbial Single-Cell RNA-Seq Analysis for Bacterial Systems

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Documentation for package ‘scProkaR’ version 0.99.3

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

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
FilterBacCells	Filter cells using bacterial QC thresholds
filter_pseudobulk_samples	Filter pseudobulk samples by size
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
PlotIntegrationOverview	Plot Seurat-style integration result panels
PlotReduction	Plot any stored reduced dimension
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_trends	Plot fitted TATA gene trends
plot_tata_gene_trend_heatmap	Plot a heatmap of 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
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
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_divergent_sce	Simulate a divergent TATA dataset
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