| add_item_to_list | Add named item (including 'NULL') to a list. |
| additional_cell_data_fn | Load additional cell data from a CSV or Rds (dataframe) file. |
| add_marker_table_links | Convert specified columns of a marker table to HTML links. |
| assert_that_ | A wrapper around 'assertthat::assert_that()'. |
| as_seurat | Convert a 'SingleCellExperiment' to 'Seurat' object. |
| calc_sc3 | Run SC3 clustering for a specific 'k'. |
| calculate_metadata | Calculate metadata for manual cell/spot annotation for... |
| cc_genes_fn | Get dataframe of cell cycle genes. |
| cell_annotation_diagnostic_plots_files_fn | Save cell annotation diagnostic plots to PDF files. |
| cell_annotation_diagnostic_plots_fn | Generate diagnostic plots for cell annotation. |
| cell_annotation_fn | Perform cell annotation via 'SingleR::SingleR()'. |
| cell_annotation_labels_fn | Create a named list of cell labels returned from... |
| cell_annotation_params_fn | Load a list of cell annotation references into a 'tibble'. |
| cell_data | Create new cell groups based on existing ones. |
| cell_data_fn | Merge all cell-related data to a single DataFrame. |
| cells_per_cluster_table | Get a frequency table of cell-cluster assignments. |
| cells_per_cluster_table_collapsed_html | Print a HTML of table collapsible by button. |
| check_pandoc | Check for 'pandoc"s binary. |
| check_pkg_installed | Check if a package is installed and display an informative... |
| check_scdrake | Check for selected 'scdrake' dependencies. |
| check_yq | Check the availability and version of the 'yq' tool. |
| cli | Install or check the command line interface scripts. |
| cluster_markers_fn | Add LFC summaries for Wilcox tests, obtained from t-test... |
| cluster_markers_heatmaps_df_fn | Create a final 'tibble' holding parameters for cluster... |
| cluster_markers_out_fn | Create a final 'dataframe' of cluster markers. |
| cluster_markers_params | Extract columns with certain parameters from cluster markers... |
| cluster_markers_params_fn | Load a list of cluster markers sources into a 'tibble'. |
| cluster_markers_processed_fn | Add additional summary columns of cluster markers for... |
| cluster_sc3_cluster_stability_plots_file_fn | Save SC3 cluster stability plots to a single PDF. |
| cluster_sc3_df_fn | Create a dataframe of SC3 clusters for a selected number of... |
| collapse_ensembl_multivals | Collapse a character vector by '","'. |
| contrasts_fn | Extract contrast statistics from cluster markers tests. |
| contrasts_heatmaps_df_fn | Create a 'tibble' holding contrast results and heatmap... |
| contrasts_out_fn | Format a 'tibble' with contrast results. |
| contrasts_params | Prepare a 'tibble' with parameters for contrasts tests. |
| create_dirs | Create a basic directory structure based on paths in config. |
| create_dummy_plot | Create a blank 'ggplot' with label. |
| create_seu_for_heatmaps | Create a 'Seurat' object used for heatmap generation. |
| create_signature_matrix_fn | Create signature matrix from provided file containing names... |
| dimred_plots_cell_annotation_params_df_fn | Make a tibble with parameters for dimred plots of cell... |
| dimred_plots_clustering_fn | Make a dimred plot for each clustering and dimred method. |
| dimred_plots_clustering_united_files_fn | Put clustering dimred plots for different parameters... |
| dimred_plots_from_params_df | Make dimred plots of selected variables. |
| dimred_plots_other_vars_params_df_fn | Make a tibble with parameters for dimred plots of selected... |
| dot-apply_config_patches | Apply YAML config patches to package-bundled configs. |
| dot-check_integration_methods | Check for valid 'INTEGRATION_SOURCES' parameter. |
| dot-check_marker_sources | Check for correct structure of 'CLUSTER_MARKERS_SOURCES' or... |
| dot-get_dict_param | Unlist a list of length one containing a named list. |
| dot-hereize_paths | Using the 'here' package, contruct paths relative to... |
| dot-load_config_group | Load a group of YAML config files. |
| dot-load_configs | Load a list of YAML config files. |
| dot-paths_to_base_dir | Construct paths relative to base directory. |
| dot-update_configs_recursive | Recursively update local configs using a file glob... |
| download_example_data | Download PBMC example data from 10x Genomics. |
| download_yq | Download the binary of the 'yq' tool (version 3.4.1). |
| empty_droplets_fn | Calculate empty droplet statistics for each cell. |
| filter_markers | Filter a dataframe with cluster markers. |
| filter_nulls | Return list with removed 'NULL' elements. |
| format_shell_command | Format a shell command as a Markdown codeblock. |
| format_used_functions | Use the '{downlit}' package to generate a Markdown list of... |
| generate_cell_annotation_plots_section | Generate a section with dimred plots used in some RMarkdown... |
| generate_dimred_plots_clustering_section | Generate a section of clustering dimensionality reduction... |
| generate_dimred_plots_section | Generate a section with dimred plots used in some RMarkdown... |
| generate_markers_results_section | Generate a table with links to marker results. |
| generate_stage_report | Render RMarkdown document for a stage of the pipeline. |
| get_cell_annotation_subplan | Get a subplan for cell annotation via 'SingleR' |
| get_clustering_graph_subplan | Get a subplan for graph-based clustering. |
| get_clustering_kmeans_subplan | Get a subplan for k-means clustering. |
| get_clustering_sc3_subplan | Get a subplan for SC3 clustering. |
| get_clustering_subplan | Get subplan for clustering. |
| get_dimred_plots_other_vars_subplan | Get a subplan for dimensionality reduction plots of selected... |
| getDistinctColors | A helper function for asigning colors in pseudotissue... |
| get_gene_filter | Get a logical filter for genes not passing a ratio of cells... |
| get_int_method_description | Return description for an integration method. |
| get_pca_gene_var_pcs | Get a number of PCs corresponding to biological variation. |
| get_pca_selected_pcs | Get a final selection of number of PCs. |
| get_plan | Get a 'drake' plan for a specific analysis type. |
| get_random_strings | Generate random strings compounded from alphabetical... |
| get_subplan_common | Get a 'drake' subplan common to all pipelines. |
| get_subplan_integration | Get a 'drake' plan for a stage of integration pipeline. |
| get_subplan_single_sample | Get a 'drake' plan for a stage of single-sample pipeline. |
| get_sys_env | Read an environment variable and if needed, assign a default... |
| get_tmp_dir | Get a path to the temporary directory according to the OS. |
| get_top_hvgs | Get top N highly variable genes (HVGs) by a specified metric. |
| get_used_qc_filters_operator_desc | Return an informative message about the used operator to join... |
| get_yq_default_path | Return a default download path for the 'yq' tool's binary. |
| grapes-and-and-grapes | A short-circuit evaluation-like function similar to 'bash"s... |
| graph_snn_fn | Compute shared nearest neighbors (SNN) graph. |
| highlight_points | Highlight points belonging to certain levels. |
| html_links | Generate a HTML link as <a></a> or in the form of image as... |
| hvg_int_list_fn | Get a named list of HVG data (gene IDs, fit, metadata). |
| hvg_plot_int_fn | Make a HVG plot for uncorrected 'SingleCellExperiment' object... |
| init_project | Initialize a new 'scdrake' project. |
| int_diagnostics_df_fn | Compute and make integration diagnostics and plots for each... |
| integration_methods_df_fn | Make a tibble with integration methods and their parameters. |
| lapply_rows | Apply a function over rows of a 'data.frame'-like object and... |
| list_names_to_values | Append names of a list of lists as values in each sublist. |
| lists_to_tibble | Convert list of lists to tibble. |
| load_config | Load a YAML config file as 'scdrake_list'. |
| load_custom_plan | Source a file returning a custom drake plan. |
| make_gene_annotation | Create a 'dataframe' with annotation of SCE object's genes... |
| make_kmeans_gaps_plot | Make a plot of k-means gaps. |
| make_pca_selected_pcs_plot | Make a plot showing numbers of selected PCs from all... |
| marker_heatmap | Make a heatmap of cell clusters. |
| marker_heatmaps_wrapper | Make a heatmap of global or contrast markers. |
| marker_plot | Make a marker plot. |
| markers_dimred_plots | Make dimred plots for each marker source defined in... |
| markers_dimred_plots_files | Save dimred plots. |
| markers_for_tables | Make a table used in HTML report of marker results. |
| markers_plots_files | Make plots of top markers. |
| markers_plots_top | Get a tibble of top markers extracted from each test result. |
| markers_table_files | Prepare a table with markers and render a HTML report from... |
| md_header | Generate a Markdown header. |
| merge_sce_metadata | Merge 'metadata()' of multiple 'SingleCellExperiment' object. |
| meta_heatmap_ploting | Manual annotation heatmap plotting |
| na_empty | Return 'NA' if an object is empty. |
| pca_phase_plots_fn | Make dimred plots of PCA colored by cell cycle phase. |
| plot_clustree | Plot clustering tree. |
| plot_colData | A wrapper for 'scater::plotColData()'. |
| plot_hvg | Plot average expression vs. HVG metrics (total, bio, and... |
| plot_hvg_fit | Plot fit of a HVG metric and highlight HVGs. |
| plotReducedDim_mod | A wrapper around 'scater::plotReducedDim()'. |
| plot_spat_point_layer_ggplot | A function for pseudotissue visualization |
| plot_spat_visuals | A function for visualization selected qc matrices in... |
| plot_vln | Make a combined violin-boxplot plot. |
| prepare_marker_source_params | Prepare a 'tibble' with parameters for cluster marker tests. |
| process_config | Config processing. |
| reexports | Objects exported from other packages |
| render_bootstrap_table | Render a dataframe-like object using 'knitr::kable()' and... |
| replace_list_nas_with_nulls | Replace 'NA's in a list by 'NULL's. |
| replace_list_nulls | Replace 'NULL' items in a defined depth of a list. |
| run_graph_based_clustering | Find clusters in SNN graph using a community detection... |
| run_kmeans_clustering | Run k-means clustering for a specific 'k'. |
| run_page_man_annotation | Calculate and run PAGE annotation. |
| run_pipeline | Run the 'scdrake' pipeline. |
| save_clustree | Save a clustree plot into PDF. |
| save_pdf | Save a list of plots to multipage PDF. |
| save_print | Capture output from 'print()' of an object. |
| save_selected_markers_plots_files | Save plots of selected markers. |
| SCDRAKE_CLI_VERSION | Matching CLI version for this package version. |
| scdrake_list | A 'scdrake"s list with overloaded, strict access operators. |
| scdrake_make | Execute a 'scdrake"s pipeline plan. |
| scdrake_options | Options used by 'scdrake'. |
| scdrake-package | scdrake: A pipeline for droplet-based single-cell RNA-seq... |
| sce_add_cell_data | Add columns to 'colData()' of a 'SingleCellExperiment'... |
| sce_add_colData | Append new columns to 'colData' of a 'SingleCellExperiment'... |
| sce_add_metadata | Append data to 'metadata()' list of a 'SingleCellExperiment'... |
| sce_add_spatial_colData | Append new columns with spatial relevance to 'colData' of a... |
| sce_calc_pca | Calculate PCA of a 'SingleCellExperiment' object. |
| sce_cc_fn | Assign cell cycle phase to cells. |
| sce_compute_dimreds | Compute t-SNE and UMAP dimreds on a 'SingleCellExperiment'... |
| sce_final_input_qc_fn | Finalize a 'SingleCellExperiment' object which will proceed... |
| sce_get_cc_genes | Identify cell cycle-related genes by using variance explained... |
| sce_history_fn | Create a tibble with history of cell and gene filtering. |
| sce_history_plot_fn | Plot history of cell and gene filtering. |
| sce_int_clustering_df_fn | Compute a quick graph-based clustering for each integration... |
| sce_int_combine_hvgs | Combine HVG data from a list of 'SingleCellExperiment'... |
| sce_int_df_fn | Perform integration of single-samples. |
| sce_int_dimred_df_fn | Calculate t-SNE and UMAP for each integration method result... |
| sce_int_dimred_plots_df_fn | Make dimred plot for each combination of integration method,... |
| sce_int_import_fn | Import 'sce_final_norm_clustering' targets from 'drake'... |
| sce_int_pca_df_fn | Compute PCA for each integration method result... |
| sce_int_processed_fn | Subset each object in a list of 'SingleCellExperiment'... |
| sce_int_raw_snn_clustering_fn | Perform a fast shared nearest neighbor clustering of each... |
| sce_norm | Normalize counts either by 'scran' or 'sctransform'. |
| sce_norm_hvg_fn | Find highly variable genes (HVGs). |
| sce_raw_fn | Import scRNA-seq data. |
| sce_remove_cc_genes | Remove cell cycle-related genes from HVGs. |
| sce_rm_doublets_fn | Remove cell doublets from a 'SingleCellExperiment' object. |
| sce_selected_fn | Select a 'SingleCellExperiment' object which will proceed to... |
| sce_valid_cells_fn | Subset cells in a 'SingleCellExperiment' object to non-empty... |
| scran_markers | Compute cell cluster markers. |
| selected_markers_dimplot | Make a grid of feature plots for selected markers. |
| selected_markers_int_df_fn | Prepare parameters for expression plots of selected markers. |
| selected_markers_int_plots_df_fn | Make expression plots of selected markers. |
| selected_markers_plots_fn | Make a grid of feature plots for selected genes. |
| set_rstudio_drake_cache | Set 'rstudio_drake_cache' option. |
| seu_add_metadata | Append data to metadata o a 'Seurat' object's assay. |
| spatGenePlot2Dsce | A function for visualization selected genes in pseudotissue... |
| text_utils_glue | Various wrappers around 'glue::glue()' and 'cat()'. |
| text_utils_joining | Various utils for joining of text. |
| update_config | Update a local YAML config file using a default one. |
| update_config_group | Update a group of configs, i.e. pipeline, single-sample, or... |
| update_project | Update 'scdrake' project files. |
| visualized_spots | A basic function for pseudotissue visualization |
| which_genes_regex | Get indices of genes whose annotation matches a regex. |
| with_dbi | Load a SQL database file and run a function from the... |
| with_plan | Locally change a 'future' plan. |
| yq_merge_cmd | Merge two YAML files using the 'yq' tool. |
