| %>% |
Man page
|
| CRUX |
Man page
|
| CRUX-package |
Man page
|
| TCGAmutations_load_with_typed_metadata |
Man page
Source code
|
| annovar_guess_reference_table |
Man page
Source code
|
| app_server |
Source code
|
| app_sys |
Source code
|
| app_ui |
Source code
|
| assert_rnaseq_df_is_formatted_correctly |
Man page
Source code
|
| assert_that_class_is_maf_data_pool |
Man page
Source code
|
| assert_that_class_is_maf_dataset_wrapper |
Man page
Source code
|
| badgify |
Man page
|
| bool_to_colour |
Man page
Source code
|
| class_is_maf_data_pool |
Man page
Source code
|
| class_is_maf_dataset_wrapper |
Man page
Source code
|
| col_1 |
Source code
|
| col_10 |
Source code
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| col_12 |
Source code
|
| col_2 |
Source code
|
| col_3 |
Source code
|
| col_4 |
Source code
|
| col_6 |
Source code
|
| col_8 |
Source code
|
| conditionalUI |
Man page
|
| create_mac_binary |
Man page
Source code
|
| create_windows_binary |
Source code
|
| curly |
Source code
|
| display |
Source code
|
| download_maf |
Man page
Source code
|
| drop_nulls |
Source code
|
| enurl |
Source code
|
| err2html |
Source code
|
| event_column_passes_sanitychecks |
Source code
|
| external_tools_add_tool_to_dataframe |
Man page
Source code
|
| external_tools_convert_expression_df_to_tumormap_return_datafram |
Source code
|
| external_tools_convert_expression_df_to_xena_expression |
Source code
|
| external_tools_convert_maf_to_bbglab |
Man page
Source code
|
| external_tools_convert_maf_to_bbglab_return_dataframe |
Man page
Source code
|
| external_tools_convert_maf_to_bed |
Source code
|
| external_tools_convert_maf_to_bed_return_dataframe |
Source code
|
| external_tools_convert_maf_to_cbioportal_mutation_mapper |
Source code
|
| external_tools_convert_maf_to_cbioportal_mutation_mapper_return_ |
Man page
Source code
|
| external_tools_convert_maf_to_cravat |
Source code
|
| external_tools_convert_maf_to_cravat_return_dataframe |
Source code
|
| external_tools_convert_maf_to_crux_maf |
Source code
|
| external_tools_convert_maf_to_cvcdap_maf |
Source code
|
| external_tools_convert_maf_to_msigdb_genelist |
Source code
|
| external_tools_convert_maf_to_msigdb_genelist_return_vec |
Source code
|
| external_tools_convert_maf_to_multiple_vanilla_vcfs |
Source code
|
| external_tools_convert_maf_to_oncodrive_return_dataframe |
Man page
Source code
|
| external_tools_convert_maf_to_one_vanilla_vcf |
Source code
|
| external_tools_convert_maf_to_proteinpaint |
Source code
|
| external_tools_convert_maf_to_proteinpaint_return_dataframe |
Source code
|
| external_tools_convert_maf_to_return_tumormap_attributes_datafra |
Source code
|
| external_tools_convert_maf_to_signal2 |
Source code
|
| external_tools_convert_maf_to_signal2_return_dataframe |
Source code
|
| external_tools_convert_maf_to_tumormap |
Source code
|
| external_tools_convert_maf_to_ucsc |
Source code
|
| external_tools_convert_maf_to_vanilla_vcf_return_dataframe |
Man page
Source code
|
| external_tools_convert_maf_to_xena |
Source code
|
| external_tools_convert_maf_to_xena_return_dataframe |
Source code
|
| external_tools_get_property_by_tool_name |
Man page
Source code
|
| external_tools_load_all_tools |
Man page
Source code
|
| external_tools_load_bbglab_cgi |
Man page
Source code
|
| external_tools_load_bbglab_oncodrive_clustl |
Man page
Source code
|
| external_tools_load_bbglab_oncodrive_fml |
Man page
Source code
|
| external_tools_load_cbioportal_mutation_mapper |
Source code
|
| external_tools_load_crux_export |
Source code
|
| external_tools_load_cvcdap_export |
Source code
|
| external_tools_load_maf_to_cravat |
Source code
|
| external_tools_load_maf_to_mutalisk_cohort_level |
Source code
|
| external_tools_load_maf_to_mutalisk_sample_level |
Source code
|
| external_tools_load_maf_to_signal2 |
Source code
|
| external_tools_load_msigdb |
Source code
|
| external_tools_load_proteinpaint |
Man page
Source code
|
| external_tools_load_tumormap |
Source code
|
| external_tools_load_ucsc |
Source code
|
| external_tools_load_xena |
Source code
|
| external_tools_update_builtin_dataset |
Man page
Source code
|
| filename_remove_extension_maf |
Source code
|
| gene_name_to_refseq_ids |
Source code
|
| gene_name_to_transcript_table |
Source code
|
| get_amino_acid_changes |
Source code
|
| get_golem_config |
Source code
|
| get_rendered_plot_height |
Man page
Source code
|
| get_rendered_plot_width |
Man page
Source code
|
| get_tcga_mafs |
Man page
|
| gistic_bad_path |
Source code
|
| gistic_check_circle |
Source code
|
| gistic_help_icon |
Source code
|
| gistic_tabulate_amp_or_del_genes_file |
Man page
Source code
|
| golem_add_external_resources |
Source code
|
| guess_genomic_mutation_filetype |
Man page
Source code
|
| html_alert |
Man page
Source code
|
| icon_down_arrow |
Man page
Source code
|
| imports |
Man page
Source code
|
| is_valid_clinicalfeaturefile |
Man page
Source code
|
| is_valid_clinicalfeaturefile_return_error |
Man page
Source code
|
| jq_hide |
Source code
|
| link |
Man page
Source code
|
| list_to_li |
Source code
|
| list_to_p |
Source code
|
| maf_data_pool_add_dataset |
Man page
Source code
|
| maf_data_pool_add_rnaseq |
Man page
Source code
|
| maf_data_pool_get_all_nonfunction_property_names |
Man page
Source code
|
| maf_data_pool_get_data_wrapper_from_unique_name |
Man page
Source code
|
| maf_data_pool_get_index_from_unique_name |
Man page
Source code
|
| maf_data_pool_get_unique_names |
Man page
Source code
|
| maf_data_pool_load_data |
Man page
Source code
|
| maf_data_pool_make_name_unique |
Man page
Source code
|
| maf_data_pool_robust_load |
Man page
Source code
|
| maf_data_pool_robust_load_apply_changes_to_reactval |
Source code
|
| maf_data_pool_to_dataframe |
Man page
Source code
|
| maf_data_pool_to_simple_dataframe |
Source code
|
| maf_data_pool_unique_name_is_available |
Man page
Source code
|
| maf_data_pool_unique_name_to_maf_nonreactive |
Man page
Source code
|
| maf_data_pool_unique_name_to_maf_reactive |
Man page
Source code
|
| maf_data_pool_unload_data |
Man page
Source code
|
| maf_data_set_wrapper_load_data |
Man page
Source code
|
| maf_data_set_wrapper_unload_data |
Man page
Source code
|
| maf_data_wrapper_add_rnaseq |
Man page
Source code
|
| maf_data_wrapper_get_rnaseq_data_for_samples_with_mutation_data |
Man page
Source code
|
| maf_data_wrapper_get_rnaseq_df |
Man page
Source code
|
| maf_data_wrapper_has_rnaseq_data |
Man page
Source code
|
| maftools_add_brca_subtype |
Man page
Source code
|
| maftools_add_clinical_data |
Man page
|
| maftools_chrom_23_and_24_to_X_and_Y |
Man page
|
| maftools_clinical_data_get_levels |
Man page
Source code
|
| maftools_clinical_data_lowest_number_of_samples_per_level |
Source code
|
| maftools_clinical_data_visually_summarise |
Man page
Source code
|
| maftools_clinical_feature_description |
Man page
|
| maftools_cluster_samples |
Man page
|
| maftools_extract_geneset_by_altered_samples |
Man page
|
| maftools_fix_clinical_data_types |
Man page
Source code
|
| maftools_get_all_data |
Man page
Source code
|
| maftools_get_transcript_refseq |
Man page
Source code
|
| maftools_maf_and_gistic_random_sample_names |
Source code
|
| maftools_maf_and_gistic_sample_name_overlap_venn |
Source code
|
| maftools_number_of_samples |
Man page
|
| maftools_plot_rainfall |
Man page
Source code
|
| maftools_remove_dubious_genes |
Man page
|
| maftools_set_difficult_aachanges_to_empty_strings |
Source code
|
| mod_cnv_server |
Source code
|
| mod_cnv_ui |
Source code
|
| mod_compare_cohorts_server |
Source code
|
| mod_compare_cohorts_ui |
Source code
|
| mod_data_import_maf_path_to_maf_server |
Man page
Source code
|
| mod_data_import_maf_path_to_maf_ui |
Man page
Source code
|
| mod_data_import_server |
Source code
|
| mod_data_import_step2_server |
Man page
Source code
|
| mod_data_import_step2_ui |
Source code
|
| mod_data_import_ui |
Source code
|
| mod_datapool_viewer_server |
Source code
|
| mod_datapool_viewer_ui |
Source code
|
| mod_druggability_server |
Source code
|
| mod_druggability_ui |
Source code
|
| mod_edit_dataset_server |
Source code
|
| mod_edit_dataset_ui |
Source code
|
| mod_expression_analysis_server |
Source code
|
| mod_expression_analysis_ui |
Source code
|
| mod_external_tools_server |
Man page
Source code
|
| mod_external_tools_ui |
Source code
|
| mod_help_server |
Source code
|
| mod_help_ui |
Source code
|
| mod_home_server |
Source code
|
| mod_home_ui |
Source code
|
| mod_import_clinical_featurefile_server |
Man page
Source code
|
| mod_import_clinical_featurefile_ui |
Man page
Source code
|
| mod_is_tcga_checkbox_server |
Source code
|
| mod_is_tcga_checkbox_ui |
Source code
|
| mod_merge_server |
Source code
|
| mod_merge_ui |
Source code
|
| mod_mutational_signatures_server |
Source code
|
| mod_mutational_signatures_ui |
Source code
|
| mod_pan_cohort_statistics_server |
Source code
|
| mod_pan_cohort_statistics_ui |
Source code
|
| mod_plot_apobec_diff_server |
Man page
Source code
|
| mod_plot_apobec_diff_ui |
Source code
|
| mod_plot_druginteractions_server |
Source code
|
| mod_plot_druginteractions_ui |
Source code
|
| mod_plot_gistic_genome_server |
Source code
|
| mod_plot_gistic_genome_ui |
Source code
|
| mod_plot_gistic_oncoplot_server |
Source code
|
| mod_plot_gistic_oncoplot_ui |
Source code
|
| mod_plot_heterogeneity_server |
Source code
|
| mod_plot_heterogeneity_ui |
Source code
|
| mod_plot_lollipop_server |
Source code
|
| mod_plot_lollipop_ui |
Man page
Source code
|
| mod_plot_maf_summary_server |
Source code
|
| mod_plot_maf_summary_ui |
Source code
|
| mod_plot_mutational_signatures_server |
Source code
|
| mod_plot_mutational_signatures_ui |
Source code
|
| mod_plot_oncogenic_pathways_focused_server |
Source code
|
| mod_plot_oncogenic_pathways_focused_ui |
Source code
|
| mod_plot_oncogenic_pathways_server |
Source code
|
| mod_plot_oncogenic_pathways_ui |
Source code
|
| mod_plot_oncoplot_server |
Source code
|
| mod_plot_oncoplot_ui |
Source code
|
| mod_plot_pfam_domains_server |
Source code
|
| mod_plot_pfam_domains_ui |
Source code
|
| mod_plot_rainfall_server |
Source code
|
| mod_plot_rainfall_ui |
Source code
|
| mod_plot_somatic_interactions_server |
Man page
Source code
|
| mod_plot_somatic_interactions_ui |
Source code
|
| mod_plot_survival_server |
Man page
Source code
|
| mod_plot_survival_ui |
Source code
|
| mod_plot_titv_graphs_server |
Source code
|
| mod_plot_titv_graphs_ui |
Source code
|
| mod_plot_tmb_in_context_of_tcga_server |
Source code
|
| mod_plot_tmb_in_context_of_tcga_ui |
Source code
|
| mod_privacy_server |
Source code
|
| mod_privacy_ui |
Source code
|
| mod_render_clinical_data_table_server |
Man page
Source code
|
| mod_render_clinical_data_table_ui |
Man page
Source code
|
| mod_render_downloadabledataframe_server |
Man page
Source code
|
| mod_render_downloadabledataframe_ui |
Source code
|
| mod_sample_level_analysis_server |
Source code
|
| mod_sample_level_analysis_ui |
Source code
|
| mod_select_genes_server |
Source code
|
| mod_select_genes_ui |
Source code
|
| mod_select_maf_clinical_data_column_server |
Source code
|
| mod_select_maf_clinical_data_column_ui |
Source code
|
| mod_select_maf_column_server |
Source code
|
| mod_select_maf_column_ui |
Source code
|
| mod_select_maf_column_value_server |
Source code
|
| mod_select_maf_column_value_ui |
Source code
|
| mod_select_maf_dataset_wrapper_server |
Man page
|
| mod_select_maf_dataset_wrapper_ui |
Source code
|
| mod_select_maf_datasets_wrapper_server |
Source code
|
| mod_select_maf_datasets_wrapper_ui |
Source code
|
| mod_select_tumor_sample_barcode_from_maf_server |
Source code
|
| mod_select_tumor_sample_barcode_from_maf_ui |
Source code
|
| mod_shinyfile_import_server |
Man page
Source code
|
| mod_shinyfile_import_ui |
Man page
Source code
|
| mod_shinyfiles_get_clinical_featurefile_path_server |
Man page
Source code
|
| mod_shinyfiles_get_clinical_featurefile_path_ui |
Man page
Source code
|
| mod_shinyfiles_get_maf_path_server |
Man page
Source code
|
| mod_shinyfiles_get_maf_path_ui |
Source code
|
| mod_single_cohort_summary_plots_server |
Source code
|
| mod_single_cohort_summary_plots_ui |
Source code
|
| mod_single_cohort_summary_tables_and_plots_server |
Man page
Source code
|
| mod_single_cohort_summary_tables_and_plots_ui |
Man page
Source code
|
| mod_single_cohort_summary_tables_server |
Source code
|
| mod_single_cohort_summary_tables_ui |
Source code
|
| mod_survival_analysis_server |
Source code
|
| mod_survival_analysis_ui |
Source code
|
| mod_tabulate_maf_server |
Source code
|
| mod_tabulate_maf_ui |
Source code
|
| mod_utility_subset_server |
Source code
|
| mod_utility_subset_ui |
Source code
|
| moduleDownloadMafServer |
Source code
|
| moduleDownloadMafUI |
Source code
|
| moduleDownloadPlotServer |
Man page
Source code
|
| moduleDownloadPlotUI |
Man page
Source code
|
| moduleEnrichmentAnalysisServer |
Source code
|
| moduleEnrichmentAnalysisUI |
Source code
|
| moduleExcludeSamplesServer |
Source code
|
| moduleExcludeSamplesUI |
Source code
|
| moduleGetColumnNameServer |
Source code
|
| moduleGetColumnNameUI |
Source code
|
| moduleIntroduceAppServer |
Source code
|
| moduleIntroduceAppUI |
Source code
|
| modulePlotCobarplotServer |
Source code
|
| modulePlotCobarplotUI |
Source code
|
| modulePlotCooncoplotServer |
Source code
|
| modulePlotCooncoplotUI |
Source code
|
| modulePlotLollipop2Server |
Source code
|
| modulePlotLollipop2UI |
Source code
|
| modulePlotRainforestServer |
Source code
|
| modulePlotRainforestUI |
Source code
|
| moduleReadMafServer |
Man page
Source code
|
| moduleReadMafUI |
Man page
Source code
|
| moduleSelectValuesFromVectorServer |
Source code
|
| moduleSelectValuesFromVectorUI |
Source code
|
| moduleSubsetByClinicalFeaturesServer |
Man page
Source code
|
| moduleSubsetByClinicalFeaturesUI |
Source code
|
| moduleUtilitiesServer |
Source code
|
| moduleUtilitiesUI |
Source code
|
| named_to_li |
Source code
|
| new_maf_data_pool |
Man page
Source code
|
| new_maf_dataset_wrapper |
Man page
Source code
|
| parse_number |
Man page
Source code
|
| path_to_default_data_pool |
Source code
|
| pcawg_dataset_to_data_pool |
Man page
Source code
|
| pcawg_dataset_to_maf_dataset_wrapper |
Man page
Source code
|
| pcawg_datasets_to_data_pool |
Man page
Source code
|
| plotforest |
Man page
Source code
|
| read_maf_flexible |
Man page
Source code
|
| read_rnaseq_file |
Man page
Source code
|
| rep_br |
Source code
|
| run_app |
Man page
Source code
|
| sample_numbers_formatted |
Source code
|
| select_gistic_help_icon |
Source code
|
| shinyInput |
Man page
Source code
|
| tagRemoveAttributes |
Source code
|
| tcga_dataset_to_data_pool |
Man page
|
| tcga_dataset_to_maf_dataset_wrapper |
Man page
Source code
|
| tcga_datasets_to_data_pool |
Man page
|
| text_is_non_zero_string |
Man page
Source code
|
| time_column_passes_sanitychecks |
Source code
|
| undisplay |
Source code
|
| update_starting_maf_data_pool |
Source code
|
| user_data_filepath_to_class_maf_dataset_wrapper |
Man page
Source code
|
| user_to_dataset_to_data_pool |
Man page
Source code
|
| with_red_star |
Source code
|
