| annotate_celltype_metrics | Annotate a SingleCellExperiment With Cell-type Metrics |
| annotate_integrated_sce | Annotate integrated, reduced dimension, and clustered... |
| annotate_merged_sce | Annotate a post-merge SingleCellExperiment with plots |
| annotate_sce | Annotate a SingleCellExperiment With Gene Names and QC... |
| annotate_sce_cells | Add basic cell-wise annotations for a SingleCellExperiment |
| annotate_sce_genes | Add basic gene-wise annotations for a SingleCellExperiment |
| cluster_sce | Cluster SingleCellExperiment with monocle3::cluster_cells |
| dot-append_cell_metric_plots_sce | Attach celltype associated metric plots to sce |
| dot-append_cell_prop_plots_sce | Attach proportional celltype plots to sce |
| dot-append_celltype_plots_sce | Helper function to plot celltypes in reduced dimensions |
| dot-append_citation_sce | Append a citation to a SingleCellExperiment |
| dot-barplot_gsea | barplot for GSEA. x axis normalizedEnrichmentScore, y axis... |
| dot-calculate_retain_parameter | helper fn - calculate the retain parameter for emptydrops... |
| dot-check_model | check model is full rank |
| dot-check_sce_for_liger | Helper function to check SCE before running liger |
| dot-clean_ggplot_plot_env | Remove objects from a ggplot plot_env |
| dot-clean_ggplot_quosures | Remove unwanted env variables from ggplot quosures |
| dot-clean_quosure_env | Remove unwanted variables from a quosure environment |
| dot-dotplot_enrichr | dotplot for ORA. x axis perturbation, y axis description |
| dot-dotplot_ora | dotplot for ORA. x axis enrichment_ratio, y axis description |
| dot-doublet_finder_plot_dim_red | plot 2d dimensionality reduction with is_doublet colour |
| dot-doublet_finder_plot_param_sweep | pparam sweep plot, pK vs BCmetricx with BCmetric maxima... |
| dot-expand_sce_rows | Helper function to expand a SingleCellExperiment to include... |
| dot-fancy_scientific | scale_y_continuous(labels=.fancy_scientific) |
| dot-filter_sce_genes_for_de | Subset a SingleCellExperiment for genes meeting expressivity... |
| dot-format_res_table_enrichr | Format result table |
| dot-format_res_table_ORA | Format result table |
| dot-formula_to_char | model formula to char/string |
| dot-generate_merge_summary_plot | helper fn to generate a merge summary plot for a... |
| dot-generate_model_from_vars | Generate a model formula from dependent, confounding, and... |
| dot-generate_pbsce_by_id | helper fn to generate a pseudobulk sce for post-merge qc |
| dot-get_d_palette | Retrieve a palette of n_colours discrete colours from... |
| dot-get_variance_explained | Get the variance explained by a variable for all genes |
| dot-get_x_most_specific_genes | Find x most specific genes |
| dot-grobify_ggplot | Clean ggplot2 env's by generating a ggplot2 grob then... |
| dot-map_celltypes | Main mapping function |
| dot-map_celltypes_with_ewce | Map cluster celltypes with EWCE |
| dot-model_fisher_celltype | Run a fisher exact test on absolute cell numbers for each... |
| dot-perform_de_with_mast | Perform DE with MAST |
| dot-perform_ks_uniformity_test | helper fn - Kolmogorov-Smirnov Uniformity Test |
| dot-plot_dirichlet_results | Plot relative celltype proportions with Dirichlet model... |
| dot-plot_emptydrops_distribution | helper fn - histogram plot to confirm uniform distribution |
| dot-plot_emptydrops_loglike | helper fn - histogram plot to confirm uniform distribution |
| dot-plot_heatmap_of_pbsce | helper fn to generate a heatmap and dendrogram for features... |
| dot-plot_n_cells_by_unique_id_var | helper fn to generate a cell numbers plot by sample |
| dot-plot_unique_id_var | Plot relative celltype proportions by sample |
| dot-prepare_dirichlet_plot_table | Prepare data for '.plot_dirichlet_results' |
| dot-prepare_fisher_counts_table | Prepare data for '.model_fisher_celltype' |
| dot-prepare_unique_id_var_plot_table | Prepare data |
| dot-preprocess_sce_for_de | Preprocess the SCE for DE analysis |
| dot-preprocess_seurat_object | temp fn |
| dot-print_citation | Print a single citation to stdout |
| dot-print_citation_html | Print a single citation to stdout as html |
| dot-process_dirichlet_fit | Process the fit model to generate an accessible summary... |
| dot-qc_append_summary_table | generate table of qc results |
| dot-qc_plot_count_depth_distribution | x axis barcode rank, y axis total counts |
| dot-qc_plot_count_depth_histogram | x axis count depth, y axis number of genes |
| dot-qc_plot_features_vs_count_depth | x axis count depth, y axis number of genes |
| dot-qc_plot_mito_fraction_histogram | x axis count depth, y axis number of genes |
| dot-qc_plot_number_genes_histogram | x axis count depth, y axis number of genes |
| dot-qc_plot_ribo_fraction_histogram | x axis count depth, y axis number of genes |
| dot-read_rds_files_to_list | Helper function to read rds files into a list |
| dot-retrieve_covariates | Retrieve the covariates from a SCE colData |
| dot-sce_to_cds | Convert a SingleCellExperiment object o a CellDataSet... |
| dot-tally_cells | Tally the cells in each celltype for each unique sample |
| dot-uniftest | Copy of archived uniftest::kolmogorov.unif.test |
| dot-with_env | Run function f in environment e |
| filter_sce | Filter SingleCellExperiment according to QC metrics Quality... |
| find_cells | Annotate a SingleCellExperiment with EmptyDrops predictions |
| find_impacted_pathways | Functional enrichment analysis |
| find_marker_genes | Find specific markers for groups of cells |
| find_singlets | Find singlets in a SingleCellExperiment |
| generate_sce | Generate a SingleCellExperiment object from a matrix and... |
| integrate_sce | Integrate datasets within a SingleCellExperiment Object |
| liger_preprocess | Preprocessing steps for Liger dimensionality reduction |
| liger_reduce_dims | Dimensionality reduction using Liger factorization |
| list_databases | Check available databases and their alias for scFlow |
| map_celltypes_sce | Map cluster celltypes with EWCE |
| map_custom_celltypes | Map Custom Celltype Annotations from a DataFrame |
| map_ensembl_gene_id | Return mappings for Ensembl Gene IDs |
| merge_sce | Merge Multiple SingleCellExperiment Objects |
| model_celltype_freqs | Model Changes in Celltype Frequencies with Dirichlet... |
| pathway_analysis_enrichr | Functional enrichment analysis using enrichR |
| pathway_analysis_webgestaltr | Functional enrichment analysis using WebgestaltR |
| perform_de | Perform Differential Gene Expression on a... |
| plot_expr_by_numeric_var | Plot Gene Expression for Samples against Numerical Variable |
| plot_reduced_dim | Plot Cells Reduced Dimensions With Feature Highlighting |
| plot_reduced_dim_gene | Plot Cells Reduced Dimensions With Gene Expression |
| plot_violin | Plot Gene Expression Violin Plots Stratified by Group |
| pseudobulk_sce | Generate a Pseudo-bulk SingleCellExperiment from a... |
| read_celltype_mappings | Read Celltype Mappings |
| read_metadata | Read the metadata for a sample from a samplesheet |
| read_sce | Read a SingleCellExperiment from a folder |
| read_sparse_matrix | Read a feature-barcode matrix |
| reduce_dims_sce | Calculate dimensionality reductions for a... |
| report_celltype_metrics | Generate A Report of Cell-Type Metrics for a... |
| report_celltype_model | Generate a report for a celltype proportion analysis |
| report_de | Generate a report for differential expression analysis |
| report_impacted_pathway | Generate a report for impacted pathway analysis |
| report_integrated_sce | Generate a report for dataset integration, dims reduction,... |
| report_merged_sce | Generate plots and a QC report for a SingleCellExperiment |
| report_qc_sce | Generate plots and a QC report for a SingleCellExperiment |
| run_doubletfinder | Find singlets in a SingleCellExperiment with DoubletFinder by... |
| sce_to_seu | temp fn |
| volcano_plot | Plot volcano plot for differential expression analysis |
| write_celltype_mappings | Write Celltype Mappings |
| write_sce | Write a SingleCellExperiment to a folder |
| write_sparse_matrix | Write a feature-barcode matrix |
