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
.Rbuildignore
.github/.gitignore
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/docker-ci.yml
.github/workflows/update-docs.yaml.disabled
.gitignore
.renvignore
CODE_OF_CONDUCT.md
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
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/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/tests.R
R/utils.R
R/utils_text.R
R/visualization.R
R/yq.R
R/zzz.R
README.Rmd
README.md
_pkgdown.yml
arm64.Dockerfile
deps.Dockerfile
dev/run_check.R
dev/run_tests.R
diagrams/README.md
diagrams/pipeline_diagram.drawio
diagrams/pipeline_diagram.pdf
diagrams/pipeline_overview.drawio
diagrams/pipeline_overview.pdf
inst/CITATION
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/common/stylesheet.css
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/gene_filtering_custom.Rmd
inst/Rmd/single_sample/01_input_qc_children/gene_filtering_qc.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/config/integration/00_main.default.yaml
inst/config/integration/01_integration.default.yaml
inst/config/integration/02_int_clustering.default.yaml
inst/config/integration/cluster_markers.default.yaml
inst/config/integration/contrasts.default.yaml
inst/config/pipeline.default.yaml
inst/config/single_sample/00_main.default.yaml
inst/config/single_sample/01_input_qc.default.yaml
inst/config/single_sample/02_norm_clustering.default.yaml
inst/config/single_sample/cluster_markers.default.yaml
inst/config/single_sample/contrasts.default.yaml
inst/extdata/selected_markers.csv
inst/plan_custom.R
inst/renv.lock
inst/scdrake
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/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/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/figures/README-unnamed-chunk-3-1.png
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/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/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_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_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_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/text_utils_glue.Rd
man/text_utils_joining.Rd
man/update_config.Rd
man/update_config_group.Rd
man/update_project.Rd
man/which_genes_regex.Rd
man/with_dbi.Rd
man/with_plan.Rd
man/yq_merge_cmd.Rd
renv.lock
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/config_test_files/config_test_1.yaml
tests/testthat/config_test_files/config_test_2.yaml
tests/testthat/config_test_files/config_test_3.yaml
tests/testthat/run_pipeline_config_patches/integration/01_integration.default.yaml
tests/testthat/run_pipeline_config_patches/integration/02_int_clustering.default.yaml
tests/testthat/run_pipeline_config_patches/integration/cluster_markers.default.yaml
tests/testthat/run_pipeline_config_patches/integration/contrasts.default.yaml
tests/testthat/run_pipeline_config_patches/integration/pipeline.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k/00_main.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k/01_input_qc.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k/pipeline.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full/00_main.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full/01_input_qc.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full/02_norm_clustering.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full/cluster_markers.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full/contrasts.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full/pipeline.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full_sct/00_main.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full_sct/01_input_qc.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full_sct/02_norm_clustering.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full_sct/cluster_markers.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full_sct/contrasts.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full_sct/pipeline.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc3k/00_main.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc3k/01_input_qc.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc3k/02_norm_clustering.default.yaml
tests/testthat/run_pipeline_config_patches/single_sample_pbmc3k/pipeline.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/integration/01_integration.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/integration/pipeline.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/single_sample_pbmc1k/01_input_qc.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/single_sample_pbmc1k/pipeline.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/single_sample_pbmc1k_modified/01_input_qc.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/single_sample_pbmc1k_modified/02_norm_clustering.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/single_sample_pbmc1k_modified/pipeline.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/single_sample_pbmc3k/01_input_qc.default.yaml
tests/testthat/run_pipeline_vignette_config_patches/single_sample_pbmc3k/pipeline.default.yaml
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.R
tests/testthat/test-run_pipeline.R
tests/testthat/test-run_pipeline_vignettes.R
tests/testthat/test-yq.R
tests/testthat/yq_test_files/dest.yaml
tests/testthat/yq_test_files/src.yaml
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_diagram.png
vignettes/pipeline_overview.Rmd
vignettes/pipeline_overview.png
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/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
