Files in bioinfocz/scdrake

A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

.github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md CODE_OF_CONDUCT.md NEWS.md R/annotation.R R/cell_annotation.R R/classes.R R/cluster_markers.R R/clustering.R R/config_load.R R/config_process_common.R R/config_process_integration.R R/config_process_single_sample.R R/config_update.R R/contrasts.R R/example_data.R R/generics.R R/html.R R/hvg.R R/integration_integration.R R/make.R R/manual_cell_annotation.R R/markers.R R/plans.R R/plans_common.R R/plans_common_cell_annotation.R R/plans_common_clustering.R R/plans_integration.R R/plans_single_sample.R R/project.R R/roxygen_helpers.R R/run.R R/scdrake-package.R R/sce.R R/single_sample_input_qc.R R/single_sample_norm_clustering.R R/spatial_visualization.R R/tests.R R/utils.R R/utils_text.R R/visualization.R R/yq.R R/zzz.R README.Rmd README.md dev/run_check.R dev/run_tests.R diagrams/README.md diagrams/pipeline_diagram.pdf diagrams/pipeline_overview.pdf inst/Rmd/common/_footer.Rmd inst/Rmd/common/_header.Rmd inst/Rmd/common/cluster_markers.Rmd inst/Rmd/common/cluster_markers_table_template.Rmd inst/Rmd/common/clustering/cluster_graph_leiden.Rmd inst/Rmd/common/clustering/cluster_graph_louvain.Rmd inst/Rmd/common/clustering/cluster_graph_walktrap.Rmd inst/Rmd/common/clustering/cluster_kmeans.Rmd inst/Rmd/common/clustering/cluster_sc3.Rmd inst/Rmd/common/clustering/clustering.Rmd inst/Rmd/common/contrasts.Rmd inst/Rmd/common/contrasts_table_template.Rmd inst/Rmd/integration/01_integration.Rmd inst/Rmd/integration/02_int_clustering.Rmd inst/Rmd/single_sample/01_input_qc.Rmd inst/Rmd/single_sample/01_input_qc_children/cell_filtering_custom.Rmd inst/Rmd/single_sample/01_input_qc_children/cell_filtering_qc.Rmd inst/Rmd/single_sample/01_input_qc_children/empty_droplets.Rmd inst/Rmd/single_sample/01_input_qc_children/empty_droplets_spat.Rmd inst/Rmd/single_sample/01_input_qc_children/gene_filtering_custom.Rmd inst/Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmd inst/Rmd/single_sample/01_input_qc_spatial.Rmd inst/Rmd/single_sample/02_norm_clustering.Rmd inst/Rmd/single_sample/02_norm_clustering_simple.Rmd inst/_drake_integration.R inst/_drake_single_sample.R inst/plan_custom.R inst/scdrake.R man/SCDRAKE_CLI_VERSION.Rd man/add_item_to_list.Rd man/add_marker_table_links.Rd man/additional_cell_data_fn.Rd man/as_seurat.Rd man/assert_that_.Rd man/calc_sc3.Rd man/calculate_metadata.Rd man/cc_genes_fn.Rd man/cell_annotation_diagnostic_plots_files_fn.Rd man/cell_annotation_diagnostic_plots_fn.Rd man/cell_annotation_fn.Rd man/cell_annotation_labels_fn.Rd man/cell_annotation_params_fn.Rd man/cell_data.Rd man/cell_data_fn.Rd man/cells_per_cluster_table.Rd man/cells_per_cluster_table_collapsed_html.Rd man/check_pandoc.Rd man/check_pkg_installed.Rd man/check_scdrake.Rd man/check_yq.Rd man/cli.Rd man/cluster_markers_fn.Rd man/cluster_markers_heatmaps_df_fn.Rd man/cluster_markers_out_fn.Rd man/cluster_markers_params.Rd man/cluster_markers_params_fn.Rd man/cluster_markers_processed_fn.Rd man/cluster_sc3_cluster_stability_plots_file_fn.Rd man/cluster_sc3_df_fn.Rd man/collapse_ensembl_multivals.Rd man/contrasts_fn.Rd man/contrasts_heatmaps_df_fn.Rd man/contrasts_out_fn.Rd man/contrasts_params.Rd man/create_dirs.Rd man/create_dummy_plot.Rd man/create_seu_for_heatmaps.Rd man/create_signature_matrix_fn.Rd man/dimred_plots_cell_annotation_params_df_fn.Rd man/dimred_plots_clustering_fn.Rd man/dimred_plots_clustering_united_files_fn.Rd man/dimred_plots_from_params_df.Rd man/dimred_plots_other_vars_params_df_fn.Rd man/dot-apply_config_patches.Rd man/dot-check_integration_methods.Rd man/dot-check_marker_sources.Rd man/dot-get_dict_param.Rd man/dot-hereize_paths.Rd man/dot-load_config_group.Rd man/dot-load_configs.Rd man/dot-paths_to_base_dir.Rd man/dot-update_configs_recursive.Rd man/download_example_data.Rd man/download_yq.Rd man/empty_droplets_fn.Rd man/filter_markers.Rd man/filter_nulls.Rd man/format_shell_command.Rd man/format_used_functions.Rd man/generate_cell_annotation_plots_section.Rd man/generate_dimred_plots_clustering_section.Rd man/generate_dimred_plots_section.Rd man/generate_markers_results_section.Rd man/generate_stage_report.Rd man/getDistinctColors.Rd man/get_cell_annotation_subplan.Rd man/get_clustering_graph_subplan.Rd man/get_clustering_kmeans_subplan.Rd man/get_clustering_sc3_subplan.Rd man/get_clustering_subplan.Rd man/get_dimred_plots_other_vars_subplan.Rd man/get_gene_filter.Rd man/get_int_method_description.Rd man/get_pca_gene_var_pcs.Rd man/get_pca_selected_pcs.Rd man/get_plan.Rd man/get_random_strings.Rd man/get_subplan_common.Rd man/get_subplan_integration.Rd man/get_subplan_single_sample.Rd man/get_sys_env.Rd man/get_tmp_dir.Rd man/get_top_hvgs.Rd man/get_used_qc_filters_operator_desc.Rd man/get_yq_default_path.Rd man/grapes-and-and-grapes.Rd man/graph_snn_fn.Rd man/highlight_points.Rd man/html_links.Rd man/hvg_int_list_fn.Rd man/hvg_plot_int_fn.Rd man/init_project.Rd man/int_diagnostics_df_fn.Rd man/integration_methods_df_fn.Rd man/lapply_rows.Rd man/list_names_to_values.Rd man/lists_to_tibble.Rd man/load_config.Rd man/load_custom_plan.Rd man/make_gene_annotation.Rd man/make_kmeans_gaps_plot.Rd man/make_pca_selected_pcs_plot.Rd man/marker_heatmap.Rd man/marker_heatmaps_wrapper.Rd man/marker_plot.Rd man/markers_dimred_plots.Rd man/markers_dimred_plots_files.Rd man/markers_for_tables.Rd man/markers_plots_files.Rd man/markers_plots_top.Rd man/markers_table_files.Rd man/md_header.Rd man/merge_sce_metadata.Rd man/meta_heatmap_ploting.Rd man/na_empty.Rd man/pca_phase_plots_fn.Rd man/plotReducedDim_mod.Rd man/plot_clustree.Rd man/plot_colData.Rd man/plot_hvg.Rd man/plot_hvg_fit.Rd man/plot_spat_point_layer_ggplot.Rd man/plot_spat_visuals.Rd man/plot_vln.Rd man/prepare_marker_source_params.Rd man/process_config.Rd man/reexports.Rd man/render_bootstrap_table.Rd man/replace_list_nas_with_nulls.Rd man/replace_list_nulls.Rd man/run_graph_based_clustering.Rd man/run_kmeans_clustering.Rd man/run_page_man_annotation.Rd man/run_pipeline.Rd man/save_clustree.Rd man/save_pdf.Rd man/save_print.Rd man/save_selected_markers_plots_files.Rd man/scdrake-package.Rd man/scdrake_list.Rd man/scdrake_make.Rd man/scdrake_options.Rd man/sce_add_cell_data.Rd man/sce_add_colData.Rd man/sce_add_metadata.Rd man/sce_add_spatial_colData.Rd man/sce_calc_pca.Rd man/sce_cc_fn.Rd man/sce_compute_dimreds.Rd man/sce_final_input_qc_fn.Rd man/sce_get_cc_genes.Rd man/sce_history_fn.Rd man/sce_history_plot_fn.Rd man/sce_int_clustering_df_fn.Rd man/sce_int_combine_hvgs.Rd man/sce_int_df_fn.Rd man/sce_int_dimred_df_fn.Rd man/sce_int_dimred_plots_df_fn.Rd man/sce_int_import_fn.Rd man/sce_int_pca_df_fn.Rd man/sce_int_processed_fn.Rd man/sce_int_raw_snn_clustering_fn.Rd man/sce_norm.Rd man/sce_norm_hvg_fn.Rd man/sce_raw_fn.Rd man/sce_remove_cc_genes.Rd man/sce_rm_doublets_fn.Rd man/sce_selected_fn.Rd man/sce_valid_cells_fn.Rd man/scran_markers.Rd man/selected_markers_dimplot.Rd man/selected_markers_int_df_fn.Rd man/selected_markers_int_plots_df_fn.Rd man/selected_markers_plots_fn.Rd man/set_rstudio_drake_cache.Rd man/seu_add_metadata.Rd man/spatGenePlot2Dsce.Rd man/text_utils_glue.Rd man/text_utils_joining.Rd man/update_config.Rd man/update_config_group.Rd man/update_project.Rd man/visualized_spots.Rd man/which_genes_regex.Rd man/with_dbi.Rd man/with_plan.Rd man/yq_merge_cmd.Rd required_libs_linux.Rmd required_libs_linux.md tests/testthat.R tests/testthat/_snaps/config.md tests/testthat/_snaps/project.md tests/testthat/_snaps/yq.md tests/testthat/setup.R tests/testthat/test-cli.R tests/testthat/test-config.R tests/testthat/test-generics.R tests/testthat/test-plans.R tests/testthat/test-project.R tests/testthat/test-run_pipeline.R tests/testthat/test-run_pipeline_vignettes.R tests/testthat/test-yq.R vignettes/_drake_parallelism.Rmd vignettes/_version.Rmd vignettes/_vignette_signpost.Rmd vignettes/config_main.Rmd vignettes/config_pipeline.Rmd vignettes/drake_basics.Rmd vignettes/pipeline_overview.Rmd vignettes/scdrake.Rmd vignettes/scdrake_advanced.Rmd vignettes/scdrake_cli.Rmd vignettes/scdrake_config.Rmd vignettes/scdrake_docker.Rmd vignettes/scdrake_envvars.Rmd vignettes/scdrake_extend.Rmd vignettes/scdrake_faq.Rmd vignettes/scdrake_integration.Rmd vignettes/scdrake_spatial.Rmd vignettes/stage_cluster_markers.Rmd vignettes/stage_contrasts.Rmd vignettes/stage_input_qc.Rmd vignettes/stage_int_clustering.Rmd vignettes/stage_integration.Rmd vignettes/stage_norm_clustering.Rmd