NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method("$",scdrake_list)
S3method("[",scdrake_list)
S3method("[[",scdrake_list)
export("%&&%")
export(SCDRAKE_CLI_VERSION)
export(add_item_to_list)
export(add_marker_table_links)
export(additional_cell_data_fn)
export(as_seurat)
export(assert_that_)
export(calc_sc3)
export(catg0)
export(catn)
export(cc_genes_fn)
export(cell_annotation_diagnostic_plots_files_fn)
export(cell_annotation_diagnostic_plots_fn)
export(cell_annotation_fn)
export(cell_annotation_labels_fn)
export(cell_annotation_params_fn)
export(cell_data_fn)
export(cells_per_cluster_table)
export(cells_per_cluster_table_collapsed_html)
export(check_cli)
export(check_clustermq_installed)
export(check_future.callr_installed)
export(check_future_installed)
export(check_pandoc)
export(check_pkg_installed)
export(check_qs_installed)
export(check_sc3_version)
export(check_scdrake)
export(check_scdrake_packages)
export(check_yq)
export(cluster_markers_fn)
export(cluster_markers_heatmap_params_fn)
export(cluster_markers_heatmaps_df_fn)
export(cluster_markers_out_fn)
export(cluster_markers_params_fn)
export(cluster_markers_plot_params_fn)
export(cluster_markers_processed_fn)
export(cluster_markers_test_params_fn)
export(cluster_sc3_cluster_stability_plots_file_fn)
export(cluster_sc3_df_fn)
export(collapse_ensembl_multivals)
export(contrasts_fn)
export(contrasts_heatmap_params_fn)
export(contrasts_heatmaps_df_fn)
export(contrasts_out_fn)
export(contrasts_params_fn)
export(contrasts_plot_params_fn)
export(create_a_link)
export(create_dummy_plot)
export(create_img_link)
export(create_integration_dirs)
export(create_seu_for_heatmaps)
export(create_signature_matrix_fn)
export(create_single_sample_dirs)
export(dimred_plots_cell_annotation_params_df_fn)
export(dimred_plots_clustering_fn)
export(dimred_plots_clustering_united_files_fn)
export(dimred_plots_from_params_df)
export(dimred_plots_other_vars_params_df_fn)
export(download_pbmc1k)
export(download_pbmc3k)
export(download_yq)
export(empty_droplets_fn)
export(filter_markers)
export(filter_nulls)
export(format_shell_command)
export(format_shell_commands)
export(format_used_functions)
export(generate_cell_annotation_plots_section)
export(generate_dimred_plots_clustering_section)
export(generate_dimred_plots_section)
export(generate_markers_results_section)
export(generate_stage_report)
export(get_cell_annotation_subplan)
export(get_cluster_markers_subplan)
export(get_clustering_graph_subplan)
export(get_clustering_kmeans_subplan)
export(get_clustering_sc3_subplan)
export(get_clustering_subplan)
export(get_common_subplan)
export(get_contrasts_subplan)
export(get_dimred_plots_other_vars_subplan)
export(get_gene_filter)
export(get_input_qc_subplan)
export(get_int_clustering_subplan)
export(get_int_method_description)
export(get_integration_plan)
export(get_integration_subplan)
export(get_norm_clustering_subplan)
export(get_pca_gene_var_pcs)
export(get_pca_selected_pcs)
export(get_random_strings)
export(get_scdrake_default_options)
export(get_scdrake_options)
export(get_single_sample_plan)
export(get_sys_env)
export(get_tmp_dir)
export(get_top_hvgs)
export(get_used_qc_filters_operator_desc)
export(get_yq_default_path)
export(glue0)
export(glue0c)
export(gluec)
export(graph_snn_fn)
export(guide_edge_colourbar)
export(highlight_points)
export(hvg_int_list_fn)
export(hvg_plot_int_fn)
export(init_project)
export(install_cli)
export(int_diagnostics_df_fn)
export(integration_methods_df_fn)
export(lapply_rows)
export(list_names_to_values)
export(lists_to_tibble)
export(load_config)
export(load_custom_plan)
export(load_integration_configs)
export(load_pipeline_config)
export(load_single_sample_configs)
export(make_cell_groupings)
export(make_gene_annotation)
export(make_kmeans_gaps_plot)
export(make_pca_selected_pcs_plot)
export(marker_heatmap)
export(marker_heatmaps_wrapper)
export(marker_plot)
export(markers_dimred_plots)
export(markers_dimred_plots_files)
export(markers_for_tables)
export(markers_plots_files)
export(markers_plots_top)
export(markers_table_files)
export(md_header)
export(merge_sce_metadata)
export(meta_heatmap_ploting)
export(na_empty)
export(pca_phase_plots_fn)
export(plotReducedDim_mod)
export(plot_clustree)
export(plot_colData)
export(plot_hvg)
export(plot_hvg_fit)
export(plot_vln)
export(render_bootstrap_table)
export(replace_list_nas_with_nulls)
export(replace_list_nulls)
export(run_graph_based_clustering)
export(run_integration)
export(run_integration_r)
export(run_kmeans_clustering)
export(run_page_man_annotation)
export(run_single_sample)
export(run_single_sample_r)
export(save_clustree)
export(save_object_info)
export(save_pdf)
export(save_print)
export(save_selected_markers_plots_files)
export(scdrake_list)
export(scdrake_make)
export(scdrake_r_make)
export(sce_add_cell_data)
export(sce_add_colData)
export(sce_add_metadata)
export(sce_calc_pca)
export(sce_cc_fn)
export(sce_compute_dimreds)
export(sce_final_input_qc_fn)
export(sce_get_cc_genes)
export(sce_history_fn)
export(sce_history_plot_fn)
export(sce_int_clustering_df_fn)
export(sce_int_combine_hvgs)
export(sce_int_df_fn)
export(sce_int_dimred_df_fn)
export(sce_int_dimred_plots_df_fn)
export(sce_int_import_fn)
export(sce_int_pca_df_fn)
export(sce_int_processed_fn)
export(sce_int_raw_snn_clustering_fn)
export(sce_norm_fn)
export(sce_norm_hvg_fn)
export(sce_raw_fn)
export(sce_remove_cc_genes)
export(sce_rm_doublets_fn)
export(sce_selected_fn)
export(sce_valid_cells_fn)
export(scran_markers)
export(scran_normalization)
export(sctransform_normalization)
export(selected_markers_dimplot)
export(selected_markers_int_df_fn)
export(selected_markers_int_plots_df_fn)
export(selected_markers_plots_fn)
export(set_rstudio_drake_cache)
export(seu_add_metadata)
export(str_comma)
export(str_line)
export(str_space)
export(update_config)
export(update_configs)
export(update_integration_configs)
export(update_pipeline_config)
export(update_project)
export(update_single_sample_configs)
export(which_genes_regex)
export(with_dbi)
export(with_plan)
export(wrap_code)
export(yq_merge_cmd)
import(BiocGenerics)
import(SingleCellExperiment)
import(SummarizedExperiment)
import(clustree)
import(patchwork)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(assertthat,are_equal)
importFrom(assertthat,assert_that)
importFrom(cli,cli)
importFrom(cli,cli_abort)
importFrom(cli,cli_alert_danger)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_alert_success)
importFrom(cli,cli_alert_warning)
importFrom(cli,cli_code)
importFrom(cli,cli_ul)
importFrom(cli,format_error)
importFrom(drake,file_in)
importFrom(drake,file_out)
importFrom(drake,ignore)
importFrom(drake,knitr_in)
importFrom(drake,target)
importFrom(drake,trigger)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,theme)
importFrom(ggraph,guide_edge_colourbar)
importFrom(glmGamPoi,glm_gp)
importFrom(glue,glue)
importFrom(here,here)
importFrom(magrittr,"%>%")
importFrom(magrittr,set_names)
importFrom(magrittr,set_rownames)
importFrom(methods,as)
importFrom(methods,is)
importFrom(rlang,"!!!")
importFrom(rlang,"!!")
importFrom(rlang,"%||%")
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,.env)
importFrom(rlang,arg_match)
importFrom(rlang,is_bare_numeric)
importFrom(rlang,is_character)
importFrom(rlang,is_empty)
importFrom(rlang,is_false)
importFrom(rlang,is_integer)
importFrom(rlang,is_list)
importFrom(rlang,is_na)
importFrom(rlang,is_null)
importFrom(rlang,is_scalar_character)
importFrom(rlang,is_true)
importFrom(rlang,sym)
importFrom(stringr,str_c)
importFrom(stringr,str_subset)
importFrom(stringr,str_to_upper)
importFrom(tibble,tibble)