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

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Search the bioinfocz/scdrake package
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Functions
445
Source code
54
Man pages
179
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bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language
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API

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

Global functions
$.scdrake_list Man page
%&&% Man page
.apply_config_patches Man page Source code
.check_duplicated_list_names Source code
.check_integration_methods Man page Source code
.check_marker_sources Man page Source code
.copy_bundled_default_configs_dir Source code
.copy_drake_file Source code
.create_common_dirs Source code
.create_dirs Source code
.create_integration_dirs Source code
.create_single_sample_dirs Source code
.default_to_local_config_file Source code
.download_raw_feature_bc_matrix Source code
.get_collapse Source code
.get_dict_param Man page Source code
.get_verbosity Source code
.hereize_paths Man page Source code
.load_config_group Man page Source code
.load_configs Man page Source code
.onAttach Source code
.onLoad Source code
.paths_to_base_dir Man page Source code
.prepare_cell_annotation_sources_params Man page
.prepare_marker_source_params Man page Source code
.prepare_marker_sources_params Man page Source code
.process_cluster_markers_config Man page Source code
.process_contrasts_config Man page
.process_input_qc_config Man page Source code
.process_int_clustering_config Man page Source code
.process_integration_config Man page Source code
.process_main_config Man page Source code
.process_norm_clustering_config Man page Source code
.process_pipeline_config Man page Source code
.run_cli Source code
.set_perm Source code
.show_postdownload_info Source code
.update_configs_recursive Man page Source code
SCDRAKE_CLI_VERSION Man page
[.scdrake_list Man page
[[.scdrake_list Man page
`$.scdrake_list` Source code
`%&&%` Source code
`[.scdrake_list` Source code
`[[.scdrake_list` Source code
add_item_to_list Man page
add_marker_table_links Man page Source code
additional_cell_data_fn Man page
as_seurat Man page Source code
assert_column_in_cell_data Source code
assert_that_ Man page Source code
calc_sc3 Man page Source code
catg0 Man page Source code
catn Man page Source code
cc_genes_fn Man page Source code
cell_annotation_diagnostic_plots_files_fn Man page Source code
cell_annotation_diagnostic_plots_fn Man page Source code
cell_annotation_fn Man page Source code
cell_annotation_labels_fn Man page Source code
cell_annotation_params_fn Man page Source code
cell_data_fn Man page
cells_per_cluster_table Man page Source code Source code
cells_per_cluster_table_collapsed_html Man page Source code
check_cli Man page
check_clustermq_installed Man page
check_future.callr_installed Man page
check_future_installed Man page
check_pandoc Man page
check_pkg_installed Man page
check_qs_installed Man page
check_sc3_version Man page
check_scdrake Man page
check_scdrake_packages Man page
check_yq Man page Source code
cluster_markers_fn Man page Source code
cluster_markers_heatmap_params_fn Man page Source code
cluster_markers_heatmaps_df_fn Man page Source code
cluster_markers_out_fn Man page Source code
cluster_markers_params_fn Man page Source code
cluster_markers_plot_params_fn Man page Source code
cluster_markers_processed_fn Man page Source code
cluster_markers_test_params_fn Man page Source code
cluster_sc3_cluster_stability_plots_file_fn Man page Source code
cluster_sc3_df_fn Man page Source code
cluster_sce_sc3_bpparam_fn Source code
collapse_ensembl_multivals Man page Source code
contrasts_fn Man page Source code
contrasts_heatmap_params_fn Man page Source code
contrasts_heatmaps_df_fn Man page Source code
contrasts_out_fn Man page Source code
contrasts_params_fn Man page Source code
contrasts_plot_params_fn Man page Source code
copy_integration_drake_file Source code
copy_single_sample_drake_file Source code
create_a_link Man page Source code
create_dummy_plot Man page
create_img_link Man page Source code
create_integration_dirs Man page Source code
create_seu_for_heatmaps Man page Source code
create_single_sample_dirs Man page Source code
dimred_plots_cell_annotation_params_df_fn Man page Source code
dimred_plots_clustering_fn Man page Source code
dimred_plots_clustering_united_files_fn Man page Source code
dimred_plots_from_params_df Man page Source code
dimred_plots_other_vars_params_df_fn Man page Source code
download_example_data Man page
download_pbmc1k Man page Source code
download_pbmc3k Man page Source code
download_yq Man page Source code
empty_droplets_fn Man page Source code
filter_ensembl_multivals_closure Source code
filter_markers Man page Source code
filter_nulls Man page
format_shell_command Man page Source code
format_shell_commands Man page Source code
format_used_functions Man page Source code
generate_cell_annotation_plots_section Man page Source code
generate_dimred_plots_clustering_section Man page Source code
generate_dimred_plots_section Man page Source code
generate_markers_results_section Man page Source code
generate_stage_report Man page Source code
get_cell_annotation_subplan Man page Source code
get_cluster_markers_subplan Man page Source code
get_clustering_graph_subplan Man page Source code
get_clustering_kmeans_subplan Man page Source code
get_clustering_sc3_subplan Man page Source code
get_clustering_subplan Man page Source code
get_common_subplan Man page Source code
get_contrasts_subplan Man page Source code
get_dimred_plots_other_vars_subplan Man page Source code
get_gene_filter Man page Source code
get_input_qc_subplan Man page Source code
get_int_clustering_subplan Man page Source code
get_int_method_description Man page
get_integration_plan Man page Source code
get_integration_subplan Man page Source code
get_norm_clustering_subplan Man page
get_pca_gene_var_pcs Man page Source code
get_pca_selected_pcs Man page Source code
get_plan Man page
get_random_strings Man page Source code
get_scdrake_default_options Man page Source code
get_scdrake_options Man page Source code
get_single_sample_plan Man page Source code
get_subplan_common Man page
get_subplan_integration Man page
get_subplan_single_sample Man page
get_sys_env Man page Source code
get_tmp_dir Man page
get_top_hvgs Man page Source code
get_used_qc_filters_operator_desc Man page Source code
get_yq_default_path Man page Source code
glue0 Man page Source code
glue0c Man page Source code
gluec Man page Source code
graph_snn_fn Man page Source code
guide_edge_colourbar Man page
highlight_points Man page Source code
hvg_int_list_fn Man page
hvg_plot_int_fn Man page
init_project Man page Source code
install_cli Man page
int_diagnostics_df_fn Man page
integration_methods_df_fn Man page
lapply_rows Man page
list_names_to_values Man page
lists_to_tibble Man page
load_config Man page Source code
load_custom_plan Man page Source code
load_integration_configs Man page Source code
load_pipeline_config Man page Source code
load_single_sample_configs Man page Source code
make_cell_groupings Man page
make_gene_annotation Man page Source code
make_kmeans_gaps_plot Man page Source code
make_pca_selected_pcs_plot Man page Source code
marker_heatmap Man page Source code
marker_heatmaps_wrapper Man page Source code
marker_plot Man page Source code
markers_dimred_plots Man page Source code
markers_dimred_plots_files Man page Source code
markers_for_tables Man page Source code
markers_plots_files Man page Source code
markers_plots_top Man page Source code
markers_table_files Man page Source code
md_header Man page Source code
merge_sce_metadata Man page Source code
na_empty Man page
pca_phase_plots_fn Man page
plotReducedDim_mod Man page Source code
plot_clustree Man page Source code
plot_colData Man page Source code
plot_hvg Man page Source code
plot_hvg_fit Man page Source code
plot_vln Man page Source code
process_config Man page
reexports Man page
render_bootstrap_table Man page Source code
replace_list_nas_with_nulls Man page
replace_list_nulls Man page Source code
run_graph_based_clustering Man page Source code
run_integration Man page Source code
run_integration_r Man page Source code
run_kmeans_clustering Man page Source code
run_pipeline Source code
run_pipeline_r Source code
run_single_sample Man page Source code
run_single_sample_r Man page Source code
save_clustree Man page Source code
save_object_info Man page
save_pdf Man page
save_print Man page
save_selected_markers_plots_files Man page Source code
scdrake Man page
scdrake-package Man page
scdrake_list Man page Source code
scdrake_make Man page Source code
scdrake_r_make Man page Source code
sce_add_cell_data Man page
sce_add_colData Man page Source code
sce_add_metadata Man page Source code
sce_calc_pca Man page Source code
sce_cc_fn Man page Source code
sce_compute_dimreds Man page Source code
sce_final_input_qc_fn Man page Source code
sce_get_cc_genes Man page Source code
sce_history_fn Man page Source code
sce_history_plot_fn Man page Source code
sce_int_clustering_df_fn Man page
sce_int_combine_hvgs Man page
sce_int_df_fn Man page
sce_int_dimred_df_fn Man page
sce_int_dimred_plots_df_fn Man page
sce_int_import_fn Man page Source code
sce_int_pca_df_fn Man page
sce_int_processed_fn Man page
sce_int_raw_snn_clustering_fn Man page
sce_norm_fn Man page Source code
sce_norm_hvg_fn Man page
sce_raw_fn Man page Source code
sce_remove_cc_genes Man page Source code
sce_rm_doublets_fn Man page
sce_selected_fn Man page Source code
sce_valid_cells_fn Man page Source code
scran_markers Man page Source code
scran_normalization Man page Source code
sctransform_normalization Man page Source code
selected_markers_dimplot Man page Source code
selected_markers_int_df_fn Man page
selected_markers_int_plots_df_fn Man page
selected_markers_plots_fn Man page
set_rstudio_drake_cache Man page
seu_add_metadata Man page Source code
str_comma Man page Source code
str_line Man page Source code
str_space Man page Source code
text_utils_glue Man page
text_utils_joining Man page
update_config Man page Source code
update_config_group Man page
update_configs Man page Source code
update_integration_configs Man page Source code
update_pipeline_config Man page Source code
update_project Man page Source code
update_single_sample_configs Man page Source code
which_genes_regex Man page Source code
with_dbi Man page Source code
with_plan Man page
wrap_code Man page Source code
yq_merge_cmd Man page Source code
bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.

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