Package index
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annotate_broad_cells() - Assign cell labels using broad-marker enrichment
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annotate_broad_clusters() - Rank cluster markers and assign broad cluster labels
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assess_cell_quality() - Assess Cell Quality Metrics
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assign_fine_labels() - Assign fine cell type labels from enrichment scores
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build_broad_marker_config() - Build broad marker configuration
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create_sce() - Create/Load a SingleCellExperiment from raw counts
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estimate_cluster_params() - Estimate clustering parameters using the cell count
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extract_top_markers() - Extract top marker genes from ranked marker tables
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find_qc_features() - Auto-detect QC feature groups
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gene_synonyms() - Retrieve gene synonyms from Ensembl
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label_broad_clusters() - Assign broad labels based on the median rank of validated markers
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load_markers() - Load and structure CellVoteR marker definitions
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normalize_counts() - Normalise counts via pooling-based size factors
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params_box() - Print a formatted box of parameters
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prepare_sce() - Prepare Analysis Tracks on a SingleCellExperiment
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print_alert() - Print a styled alert message
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print_h1() - Print a styled H1 header with optional contextual information
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print_h2() - Print a styled H2 header
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print_inline_vec() - Print an inline vector summary
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print_status_bar() - Print a status bar with icons
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rank_cluster_markers() - Rank markers for each cluster using scran::findMarkers()
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resolve_consensus_labels() - Resolve final cell labels via majority vote
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run_cellvoter() - Run the CellVoteR ensemble annotation pipeline
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score_markers_against_panel() - Score cluster marker genes against fine cell type marker panels
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step_fmt() - Format text for the CLI progress steps
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subcluster_labels() - Generate subcluster labels within broad cell groups