Nuclei Analysis Toolkit

Global functions
.append_cell_metric_plots_sce	Man page Source code
.append_cell_prop_plots_sce	Man page Source code
.append_celltype_plots_sce	Man page
.append_citation_sce	Man page Source code
.barplot_gsea	Man page
.calculate_retain_parameter	Man page Source code
.check_model	Man page
.check_sce_for_liger	Man page Source code
.clean_ggplot_plot_env	Man page Source code
.clean_ggplot_quosures	Man page
.clean_quosure_env	Man page
.dotplot_enrichr	Man page
.dotplot_ora	Man page Source code
.doublet_finder_plot_dim_red	Man page
.doublet_finder_plot_param_sweep	Man page
.expand_sce_rows	Man page
.fancy_scientific	Man page
.filter_sce_genes_for_de	Man page
.format_res_table_GSEA	Source code
.format_res_table_ORA	Man page Source code
.format_res_table_enrichr	Man page
.formula_to_char	Man page
.generate_kbet_plot	Source code
.generate_merge_summary_plot	Man page
.generate_model_from_vars	Man page
.generate_pbsce_by_id	Man page Source code
.generate_upset_plot	Source code
.get_d_palette	Man page
.get_variance_explained	Man page
.get_x_most_specific_genes	Man page
.grobify_ggplot	Man page Source code
.map_celltypes	Man page
.map_celltypes_with_ewce	Man page
.model_fisher_celltype	Man page Source code
.perform_de_with_mast	Man page Source code
.perform_ks_uniformity_test	Man page Source code
.plot_dirichlet_results	Man page Source code
.plot_emptydrops_distribution	Man page Source code
.plot_emptydrops_loglike	Man page Source code
.plot_heatmap_of_pbsce	Man page Source code
.plot_n_cells_by_unique_id_var	Man page
.plot_unique_id_var	Man page Source code
.prepare_dirichlet_plot_table	Man page Source code
.prepare_fisher_counts_table	Man page Source code
.prepare_plot_dt	Source code
.prepare_unique_id_var_plot_table	Man page Source code
.prepare_volcano_plot_dt	Source code
.prepare_zero_prop_plot	Source code
.preprocess_sce_for_de	Man page Source code
.preprocess_seurat_object	Man page
.print_citation	Man page Source code
.print_citation_html	Man page Source code
.process_dirichlet_fit	Man page Source code
.qc_append_summary_table	Man page
.qc_plot_count_depth_distribution	Man page
.qc_plot_count_depth_histogram	Man page
.qc_plot_features_vs_count_depth	Man page
.qc_plot_mito_fraction_histogram	Man page
.qc_plot_number_genes_histogram	Man page
.qc_plot_ribo_fraction_histogram	Man page
.read_rds_files_to_list	Man page
.retrieve_covariates	Man page Source code
.run_tsne	Source code
.run_umap	Source code
.scatter_plot	Source code
.sce_to_cds	Man page Source code
.tally_cells	Man page Source code
.uniftest	Man page
.volcano_plot_fn	Source code
.with_env	Man page Source code
and_list_fn	Source code
annotate_celltype_metrics	Man page Source code
annotate_integrated_sce	Man page Source code
annotate_merged_sce	Man page Source code
annotate_sce	Man page Source code
annotate_sce_cells	Man page Source code
annotate_sce_genes	Man page Source code
cluster_sce	Man page Source code
filter_sce	Man page Source code
find_cells	Man page Source code
find_impacted_pathways	Man page Source code
find_marker_genes	Man page Source code
find_singlets	Man page Source code
generate_sce	Man page Source code
integrate_sce	Man page Source code
liger_preprocess	Man page Source code
liger_reduce_dims	Man page Source code
list_databases	Man page Source code
map_celltypes_sce	Man page Source code
map_custom_celltypes	Man page Source code
map_ensembl_gene_id	Man page Source code
merge_sce	Man page Source code
model_celltype_freqs	Man page Source code
pathway_analysis_enrichr	Man page Source code
pathway_analysis_webgestaltr	Man page Source code
perform_de	Man page Source code
plot_expr_by_numeric_var	Man page Source code
plot_reduced_dim	Man page Source code
plot_reduced_dim_gene	Man page Source code
plot_violin	Man page Source code
pseudobulk_sce	Man page Source code
read_celltype_mappings	Man page Source code
read_metadata	Man page Source code
read_sce	Man page Source code
read_sparse_matrix	Man page Source code
reduce_dims_sce	Man page Source code
report_celltype_metrics	Man page Source code
report_celltype_model	Man page Source code
report_de	Man page Source code
report_impacted_pathway	Man page Source code
report_integrated_sce	Man page Source code
report_merged_sce	Man page Source code
report_qc_sce	Man page Source code
run_doubletfinder	Man page Source code
sce_to_seu	Man page Source code
volcano_plot	Man page Source code
write_celltype_mappings	Man page Source code
write_sce	Man page Source code
write_sparse_matrix	Man page Source code