Files in CCICB/CRUX
Easily explore patterns of somatic variation in cancer using 'CRUX'

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/R-CMD-check.yaml

.gitignore

.rscignore

CODE_OF_CONDUCT.md

CRUX.Rproj

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

NOTICE

R/CRUX-package.R R/GLOBALS.R R/_disable_autoload.R R/app_config.R R/app_server.R R/app_ui.R R/class_maf_data_pool.R R/class_maf_dataset_wrapper.R R/data.R R/data_loading_utils.R R/data_wrapping_pcawg.R R/data_wrapping_tcga.R R/data_wrapping_user_imports.R R/fct_TCGAmutations_load_with_typed_metadata.R R/fct_centered_down_arrow.R R/fct_download_maf.R R/fct_external_tools_load_dataframe.R R/fct_filetype_guesser.R R/fct_gistic.R R/fct_maftools_extending_functions.R R/fct_maftools_fix_clinical_data_types.R R/golem_utils_server.R R/golem_utils_ui.R R/helper_functions.R R/mod_cnv.R R/mod_compare_cohorts.R R/mod_data_import.R R/mod_data_import_maf_path_to_maf.R R/mod_data_import_step2.R R/mod_data_pool_table.R

R/mod_download_datatable.R

R/mod_download_maf.R R/mod_download_plot.R R/mod_druggability.R R/mod_edit_dataset.R R/mod_enrichment.R R/mod_exclude_samples.R R/mod_expression_analysis.R R/mod_expression_import.R R/mod_external_tools.R R/mod_help.R R/mod_home.R R/mod_import_clinical_featurefile.R R/mod_import_maf.R R/mod_introduce_app.R R/mod_is_tcga_checkbox.R R/mod_load_tcga.R R/mod_merge.R R/mod_mod_select_maf_datasets_wrapper.R R/mod_mutational_signatures.R R/mod_pan_cohort_statistics.R R/mod_plot_apobec_diff.R R/mod_plot_cobarplot.R R/mod_plot_complete_pathway.R R/mod_plot_cooncoplots.R R/mod_plot_druginteractions.R R/mod_plot_gistic_genome.R R/mod_plot_gistic_oncoplot.R R/mod_plot_heterogeneity.R R/mod_plot_lollipop.R R/mod_plot_lollipop2.R R/mod_plot_mutational_signatures.R R/mod_plot_oncogenic_pathways.R R/mod_plot_oncoplots.R R/mod_plot_pfam_domains.R R/mod_plot_rainfall.R R/mod_plot_rainforest.R R/mod_plot_somatic_interactions.R R/mod_plot_summary.R R/mod_plot_survival.R R/mod_plot_tcgacompare.R R/mod_plot_titv.R R/mod_plot_tsne.R R/mod_privacy.R R/mod_render_clinical_data_table.R R/mod_render_downloadable_dataframe.R R/mod_sample_level_analysis.R R/mod_select_column_from_dataframe.R R/mod_select_dataset_from_maf_data_pool_pickerinput_and_return_maf_dataset_wrapper.R R/mod_select_genes.R R/mod_select_maf_column.R R/mod_select_maf_column_value.R R/mod_select_tumor_sample_barcode_from_maf.R R/mod_select_value_from_vector.R R/mod_shinyfile_import.R R/mod_shinyfiles_get_clinical_featurefile_path.R R/mod_shinyfiles_get_maf_path.R R/mod_single_cohort_summary.R R/mod_split_maf_by_clinical_feature.R R/mod_survival_analysis.R R/mod_tabulate_maf.R R/mod_utilities.R R/mod_utility_subset.R R/run_app.R R/update_starting_maf_data_pool.R R/utils-pipe.R R/utils_bool_to_colour.R R/utils_error_messages.R R/utils_installation.R R/utils_links.R

R/utils_spacer.R

R/utils_text_is_valid_input.R R/utils_validating_clinical_feature_files.R R/visualise_data_pool.R README.md app.R dev/01_start.R dev/02_dev.R dev/03_deploy.R dev/run_dev.R

inst/app/css_themes_hidden_away/bootstrap.darkly.css

inst/app/css_themes_hidden_away/bootstrap.minty.css

inst/app/css_themes_hidden_away/bootstrap.superhero.css

inst/app/img/landing_page.png

inst/app/img/landing_page_subset.png

inst/app/img/workflows.png

inst/app/www/favicon.ico

inst/default_data_pool.Rds

inst/example_data/APL_primary.maf

inst/example_data/APL_primary.maf.gz

inst/example_data/APL_primary_and_relapse.clinical_features.tsv

inst/example_data/APL_primary_and_relapse.maf

inst/example_data/APL_relapse.maf.gz

inst/example_data/blca_rnaseq.tsv

inst/example_data/brca.maf.gz

inst/example_data/demo.multisample.vcf

inst/example_data/gistic/tcga_gbm/all_lesions.conf_99.txt

inst/example_data/gistic/tcga_gbm/amp_genes.conf_99.txt

inst/example_data/gistic/tcga_gbm/del_genes.conf_99.txt

inst/example_data/gistic/tcga_gbm/scores.gistic

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2789_lung.squamous.cell.carcinoma_5_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2789_lung.squamous.cell.carcinoma_5_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2791_lung.squamous.cell.carcinoma_5_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2791_lung.squamous.cell.carcinoma_5_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2792_lung.squamous.cell.carcinoma_4_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2792_lung.squamous.cell.carcinoma_4_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2793_lung.squamous.cell.carcinoma_2_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2793_lung.squamous.cell.carcinoma_2_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2794_lung.squamous.cell.carcinoma_3_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2794_lung.squamous.cell.carcinoma_3_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2795_lung.squamous.cell.carcinoma_4_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2795_lung.squamous.cell.carcinoma_4_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2800_lung.squamous.cell.carcinoma_3_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-66-2800_lung.squamous.cell.carcinoma_3_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-70-6722_lung.squamous.cell.carcinoma_4_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-70-6722_lung.squamous.cell.carcinoma_4_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-70-6723_lung.squamous.cell.carcinoma_3_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-70-6723_lung.squamous.cell.carcinoma_3_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-85-6175_lung.squamous.cell.carcinoma_2_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-85-6175_lung.squamous.cell.carcinoma_2_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-85-6560_lung.squamous.cell.carcinoma_5_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-85-6560_lung.squamous.cell.carcinoma_5_report.txt

inst/example_data/lusc_tcga/mutalisk_input_TCGA-85-6561_lung.squamous.cell.carcinoma_3_report.pdf

inst/example_data/lusc_tcga/mutalisk_input_TCGA-85-6561_lung.squamous.cell.carcinoma_3_report.txt

inst/example_data/multianno.clinical_features.tsv

inst/example_data/nonstandard_vaf_and_protein_change_column_names.large.maf

inst/example_data/nonstandard_vaf_and_protein_change_column_names.maf

inst/example_data/scores.gistic

inst/example_data/tcga_laml.maf.gz

inst/example_data/tcga_laml_annot.tsv

inst/example_data/variants.hg19_multianno.txt

inst/extdata/files_required_for_tmb_comparison/TCGA_cohorts

inst/extdata/files_required_for_tmb_comparison/TCGA_primary_site

inst/external_tool_metadata_readme

inst/golem-config.yml

inst/logos/CRUX_hex.300ppi.png

inst/logos/CRUX_hex.72ppi.png

inst/logos/CRUX_hex.pdf

inst/logos/CRUX_hex_512_512.72ppi.icns

inst/logos/CRUX_hex_512_512.72ppi.png

inst/logos/CRUX_hex_512_512.pdf

inst/logos/logo_CGI.png

inst/logos/support_organisations_extensive_wide.png

inst/test_data/external_data_conversion_cgi_out.tsv

inst/test_data/external_data_conversion_input.maf.gz

inst/test_data/invalid.maf

inst/test_data/tcga_laml.subsampled.maf.gz

inst/test_data/tcga_laml.subsampled.maf.sorted

inst/test_data/tcga_laml.subsubsampled.maf.gz

inst/test_data/tcga_laml_annot.csv

inst/test_data/tcga_laml_annot.duplicated_tumor_sample_barcode.tsv

inst/test_data/tcga_laml_annot.extra_tumor_sample_barcodes.tsv

inst/test_data/tcga_laml_annot.missing_tumor_sample_barcode.tsv

inst/test_data/tcga_laml_annot.no_tumor_sample_barcode.tsv

inst/test_data/tcga_laml_annot.only_tumor_sample_barcodes.tsv

inst/test_data/tcga_laml_annot.tsv

inst/test_data/test_cgi_export.tsv

inst/test_data/test_download_maf.maf

man/figures/logo.png

man/get_rendered_plot_height.Rd man/get_rendered_plot_width.Rd man/get_tcga_mafs.Rd man/gistic_tabulate_amp_or_del_genes_file.Rd man/guess_genomic_mutation_filetype.Rd man/html_alert.Rd man/icon_down_arrow.Rd man/imports.Rd man/is_valid_clinicalfeaturefile.Rd man/is_valid_clinicalfeaturefile_return_error.Rd man/link.Rd man/maf_data_pool_add_dataset.Rd man/maf_data_pool_add_rnaseq.Rd man/maf_data_pool_get_all_nonfunction_property_names.Rd man/maf_data_pool_get_data_wrapper_from_unique_name.Rd man/maf_data_pool_get_index_from_unique_name.Rd man/maf_data_pool_get_unique_names.Rd man/maf_data_pool_load_data.Rd man/maf_data_pool_make_name_unique.Rd man/maf_data_pool_robust_load.Rd man/maf_data_pool_to_dataframe.Rd man/maf_data_pool_unique_name_is_available.Rd man/maf_data_pool_unique_name_to_maf_nonreactive.Rd man/maf_data_pool_unique_name_to_maf_reactive.Rd man/maf_data_pool_unload_data.Rd man/maf_data_set_wrapper_load_data.Rd man/maf_data_set_wrapper_unload_data.Rd man/maf_data_wrapper_add_rnaseq.Rd man/maf_data_wrapper_get_rnaseq_data_for_samples_with_mutation_data.Rd man/maf_data_wrapper_get_rnaseq_df.Rd man/maf_data_wrapper_has_rnaseq_data.Rd man/maftools_add_brca_subtype.Rd man/maftools_add_clinical_data.Rd man/maftools_chrom_23_and_24_to_X_and_Y.Rd man/maftools_clinical_data_get_levels.Rd man/maftools_clinical_data_visually_summarise.Rd man/maftools_clinical_feature_description.Rd man/maftools_cluster_samples.Rd man/maftools_extract_geneset_by_altered_samples.Rd man/maftools_fix_clinical_data_types.Rd man/maftools_get_all_data.Rd man/maftools_get_transcript_refseq.Rd man/maftools_number_of_samples.Rd man/maftools_plot_rainfall.Rd man/maftools_remove_dubious_genes.Rd man/mod_data_import_maf_path_to_maf_server.Rd man/mod_data_import_maf_path_to_maf_ui.Rd man/mod_data_import_step2_server.Rd man/mod_external_tools_server.Rd man/mod_import_clinical_featurefile_server.Rd man/mod_import_clinical_featurefile_ui.Rd man/mod_plot_apobec_diff_server.Rd man/mod_plot_lollipop_ui.Rd man/mod_plot_somatic_interactions_server.Rd man/mod_plot_survival_server.Rd man/mod_render_clinical_data_table_server.Rd man/mod_render_clinical_data_table_ui.Rd man/mod_render_downloadabledataframe_server.Rd man/mod_select_maf_dataset_wrapper_server.Rd man/mod_shinyfile_import_server.Rd man/mod_shinyfile_import_ui.Rd man/mod_shinyfiles_get_clinical_featurefile_path_server.Rd man/mod_shinyfiles_get_clinical_featurefile_path_ui.Rd man/mod_shinyfiles_get_maf_path_server.Rd man/mod_single_cohort_summary_tables_and_plots_server.Rd man/mod_single_cohort_summary_tables_and_plots_ui.Rd man/moduleDownloadPlotServer.Rd man/moduleDownloadPlotUI.Rd man/moduleReadMafServer.Rd man/moduleReadMafUI.Rd man/moduleSubsetByClinicalFeaturesServer.Rd man/new_maf_data_pool.Rd man/new_maf_dataset_wrapper.Rd man/parse_number.Rd man/pcawg_dataset_to_data_pool.Rd man/pcawg_dataset_to_maf_dataset_wrapper.Rd man/pcawg_datasets_to_data_pool.Rd man/pipe.Rd man/plotforest.Rd man/read_maf_flexible.Rd man/read_rnaseq_file.Rd man/run_app.Rd man/shinyInput.Rd man/tcga_dataset_to_data_pool.Rd man/tcga_dataset_to_maf_dataset_wrapper.Rd man/tcga_datasets_to_data_pool.Rd man/text_is_non_zero_string.Rd man/user_data_filepath_to_class_maf_dataset_wrapper.Rd man/user_to_dataset_to_data_pool.Rd

rsconnect/shinyapps.io/ccicb/crux.dcf

CCICB/CRUX documentation built on Jan. 28, 2024, 10:12 p.m.

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CCICB/CRUX
Easily explore patterns of somatic variation in cancer using 'CRUX'

Files in CCICB/CRUX
Easily explore patterns of somatic variation in cancer using 'CRUX'

R Package Documentation

Browse R Packages

We want your feedback!

CCICB/CRUX Easily explore patterns of somatic variation in cancer using 'CRUX'

Files in CCICB/CRUX Easily explore patterns of somatic variation in cancer using 'CRUX'

R Package Documentation

Browse R Packages

We want your feedback!

CCICB/CRUX
Easily explore patterns of somatic variation in cancer using 'CRUX'

Files in CCICB/CRUX
Easily explore patterns of somatic variation in cancer using 'CRUX'