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  "Title": "Microbial Single-Cell RNA-Seq Analysis for Bacterial Systems",
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  "Description": "scProkaR provides a SingleCellExperiment-centred workflow\nfor microbial single-cell RNA sequencing data. It standardises\nbacterial input objects from count matrices, 10x Genomics\ndirectories or Seurat objects, and computes prokaryote-specific\nquality-control metrics such as ribosomal RNA fraction. It\nperforms batch integration with several backends and scores the\nresulting embeddings with scIB-inspired benchmarking metrics.\nIt also supports pseudobulk differential expression with edgeR\nand Time Aware Trajectory Analysis (TATA), a time-informed\ntrajectory abstraction for perturbation time courses.",
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    "PlotReduction",
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    "RunIntegratedClustering",
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    "simulate_tata_multidrug_sce",
    "simulate_tata_sce",
    "simulate_tata_spiral_sce"
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      "title": "Example bacterial single-cell dataset",
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      "file": "sce1.rda",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
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      "page": "adjacent_timepoint_auc",
      "title": "Compute adjacent-timepoint AUC for a pseudotime ordering",
      "topics": [
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      ]
    },
    {
      "page": "aggregate_pseudobulk",
      "title": "Aggregate single-cell data into pseudobulk samples",
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    },
    {
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      "title": "Measure the weight of anti-causal edges in a directed graph",
      "topics": [
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      ]
    },
    {
      "page": "BenchmarkIntegration",
      "title": "Benchmark integration quality with scIB-inspired metrics",
      "topics": [
        "BenchmarkIntegration"
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    },
    {
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    },
    {
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      "title": "Build a cell-cell kNN graph",
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      "topics": [
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      "title": "Cluster graph-connected cell states",
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      "title": "Compute TATA branch probabilities and entropy",
      "topics": [
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    },
    {
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      "title": "Compute branch-specific TATA gene trends",
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    {
      "page": "compute_tata_pseudotime",
      "title": "Compute TATA pseudotime",
      "topics": [
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    },
    {
      "page": "compute_time_weights",
      "title": "Compute time consistency for cluster-cluster edges",
      "topics": [
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    },
    {
      "page": "compute_topology_weights",
      "title": "Compute topology-based cluster connectivity weights",
      "topics": [
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    },
    {
      "page": "CreateBacObject",
      "title": "Create a standardized bacterial single-cell object",
      "topics": [
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      ]
    },
    {
      "page": "directed_reachability_concordance",
      "title": "Quantify how well a directed cluster graph follows real time",
      "topics": [
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    },
    {
      "page": "filter_pseudobulk_samples",
      "title": "Filter pseudobulk samples by size",
      "topics": [
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    },
    {
      "page": "FilterBacCells",
      "title": "Filter cells using bacterial QC thresholds",
      "topics": [
        "FilterBacCells"
      ]
    },
    {
      "page": "IntegrateBacData",
      "title": "Integrate microbial single-cell batches",
      "topics": [
        "IntegrateBacData"
      ]
    },
    {
      "page": "local_temporal_order_metrics",
      "title": "Compute local temporal order metrics on a cell graph",
      "topics": [
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      ]
    },
    {
      "page": "MergeBacObjects",
      "title": "Merge multiple scProkaR or SingleCellExperiment objects",
      "topics": [
        "MergeBacObjects"
      ]
    },
    {
      "page": "normalize_pseudobulk",
      "title": "Normalize pseudobulk samples for exploratory analysis",
      "topics": [
        "normalize_pseudobulk"
      ]
    },
    {
      "page": "orient_pseudotime_to_time",
      "title": "Orient pseudotime to match increasing real time",
      "topics": [
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      ]
    },
    {
      "page": "plot_pairwise_de_ma",
      "title": "Plot an MA plot for a pairwise edgeR contrast",
      "topics": [
        "plot_pairwise_de_ma"
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    },
    {
      "page": "plot_pairwise_de_volcano",
      "title": "Plot a volcano plot for a pairwise edgeR contrast",
      "topics": [
        "plot_pairwise_de_volcano"
      ]
    },
    {
      "page": "plot_tata_branch_confusion",
      "title": "Plot truth versus inferred TATA branch assignments",
      "topics": [
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    },
    {
      "page": "plot_tata_branch_probabilities",
      "title": "Plot TATA branch probabilities on an embedding",
      "topics": [
        "plot_tata_branch_probabilities"
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    },
    {
      "page": "plot_tata_branch_selection",
      "title": "Plot selected cells from one TATA branch",
      "topics": [
        "plot_tata_branch_selection"
      ]
    },
    {
      "page": "plot_tata_cluster_graph",
      "title": "Plot the cluster-level TATA graph",
      "topics": [
        "plot_tata_cluster_graph"
      ]
    },
    {
      "page": "plot_tata_edge_causality",
      "title": "Plot TATA edge causality diagnostics",
      "topics": [
        "plot_tata_edge_causality"
      ]
    },
    {
      "page": "plot_tata_gene_trend_heatmap",
      "title": "Plot a heatmap of TATA gene trends",
      "topics": [
        "plot_tata_gene_trend_heatmap"
      ]
    },
    {
      "page": "plot_tata_gene_trends",
      "title": "Plot fitted TATA gene trends",
      "topics": [
        "plot_tata_gene_trends"
      ]
    },
    {
      "page": "plot_tata_results",
      "title": "Plot an overview of TATA results",
      "topics": [
        "plot_tata_results"
      ]
    },
    {
      "page": "plot_tata_terminal_probabilities",
      "title": "Plot branch probabilities for representative cells",
      "topics": [
        "plot_tata_terminal_probabilities"
      ]
    },
    {
      "page": "plot_tata_time_calibration",
      "title": "Plot TATA time calibration",
      "topics": [
        "plot_tata_time_calibration"
      ]
    },
    {
      "page": "plot_tata_trajectory_embedding",
      "title": "Plot TATA trajectories over an embedding",
      "topics": [
        "plot_tata_trajectory_embedding"
      ]
    },
    {
      "page": "plot_time_series_deg_curves",
      "title": "Plot fitted spline expression curves from time-series DE",
      "topics": [
        "plot_time_series_deg_curves"
      ]
    },
    {
      "page": "PlotIntegrationOverview",
      "title": "Plot Seurat-style integration result panels",
      "topics": [
        "PlotIntegrationOverview"
      ]
    },
    {
      "page": "PlotReduction",
      "title": "Plot any stored reduced dimension",
      "topics": [
        "PlotReduction"
      ]
    },
    {
      "page": "RegisterExistingIntegrationEmbeddings",
      "title": "Register existing reduced dimensions as integration embeddings",
      "topics": [
        "RegisterExistingIntegrationEmbeddings"
      ]
    },
    {
      "page": "RegisterIntegrationEmbedding",
      "title": "Register an external embedding for benchmarking and downstream analysis",
      "topics": [
        "RegisterIntegrationEmbedding"
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    },
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      "page": "run_edger_pairwise_de",
      "title": "Run pairwise pseudobulk differential expression with edgeR",
      "topics": [
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      "page": "run_edger_spline_de",
      "title": "Run pseudobulk spline or time-series differential expression with edgeR",
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    },
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      "title": "Run a full scProkaR differential expression workflow",
      "topics": [
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    {
      "page": "run_tata",
      "title": "Run the full TATA workflow",
      "topics": [
        "run_tata"
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    },
    {
      "page": "RunBacQC",
      "title": "Compute bacterial QC metrics",
      "topics": [
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    },
    {
      "page": "RunIntegratedClustering",
      "title": "Cluster cells on an integrated embedding",
      "topics": [
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    },
    {
      "page": "RunIntegratedUMAP",
      "title": "Run UMAP on an existing embedding",
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    },
    {
      "page": "sce1",
      "title": "Example bacterial single-cell dataset",
      "topics": [
        "sce1"
      ]
    },
    {
      "page": "select_tata_branch_cells",
      "title": "Select cells from a TATA branch",
      "topics": [
        "select_tata_branch_cells"
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    },
    {
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      "title": "Simulate a multi-drug branching TATA dataset",
      "topics": [
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    },
    {
      "page": "simulate_tata_sce",
      "title": "Simulate a divergent TATA dataset",
      "topics": [
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        "simulate_tata_sce"
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    },
    {
      "page": "simulate_tata_spiral_sce",
      "title": "Simulate an extreme spiral-plus-divergent TATA dataset",
      "topics": [
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      ]
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