Files in cannin/tumorcomparer

Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity

.Rbuildignore

.binder/Dockerfile

.binder/installPackages.R

.binder/r-requirements.dcf

.github/.gitignore

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

.github/workflows/docker.yml

.gitignore

DESCRIPTION

Dockerfile

LICENSE

NAMESPACE

R/ballon_plot_data_to_result_table.R R/calc_weighted_corr.R R/categorize_cell_lines.R R/compute_freq_alt.R R/convert_to_0_to_1_using_xminusmin_by_maxminusmin.R R/cyj_graph_maker_from_dist_mat.R R/data.R R/generate_composite_mat_and_gene_weights.R R/graphNELtoJSON.R R/keep_only_high_level_cnas.R R/make_balloon_plot_data_from_comparison_result.R R/make_balloon_plot_data_from_mtc.R R/map_mean_similarity_to_gradient.R R/pair_dist.R R/plot_balloon_plot.R R/plot_joyplot.R R/plot_mds.R R/return_first_part.R R/run_comparison.R R/run_comparison_config_list.R R/run_shiny_app.R R/tc_geneset_comparison.R R/tic_toc.R README.md

TumorComparer.Rproj

data/tcga_pancan_pathway_genes.rda

inst/cbioportal_ccle/CCLP_ID_and_Cancer_Type.txt

inst/cbioportal_ccle/ccle_cclp_cbioportal_mapping.txt

inst/cbioportal_ccle/cellline_ccle_broad_clinical_data.tsv

inst/cbioportal_ccle/make_cclp_cbioportal_mapping.R

inst/extdata/LIHC_data.zip

inst/extdata/READ_data_for_running_TC.zip

inst/extdata/READ_data_for_running_TC/Genes_and_weights_cna.txt

inst/extdata/READ_data_for_running_TC/Genes_and_weights_exp.txt

inst/extdata/READ_data_for_running_TC/Genes_and_weights_mut.txt

inst/extdata/READ_data_for_running_TC/cell_line_cna.txt

inst/extdata/READ_data_for_running_TC/cell_line_exp.txt

inst/extdata/READ_data_for_running_TC/cell_line_mut.txt

inst/extdata/READ_data_for_running_TC/default_weights_for_known_cancer_genes_cna.txt

inst/extdata/READ_data_for_running_TC/default_weights_for_known_cancer_genes_exp.txt

inst/extdata/READ_data_for_running_TC/default_weights_for_known_cancer_genes_mut.txt

inst/extdata/READ_data_for_running_TC/tumor_cna.txt

inst/extdata/READ_data_for_running_TC/tumor_exp.txt

inst/extdata/READ_data_for_running_TC/tumor_mut.txt

inst/extdata/mock_5_data_types.tar.gz

inst/extdata/mock_5_data_types/Genes_and_weights_cna.txt

inst/extdata/mock_5_data_types/Genes_and_weights_exp.txt

inst/extdata/mock_5_data_types/Genes_and_weights_meth.txt

inst/extdata/mock_5_data_types/Genes_and_weights_mut.txt

inst/extdata/mock_5_data_types/Genes_and_weights_prot.txt

inst/extdata/mock_5_data_types/cell_line_cna.txt

inst/extdata/mock_5_data_types/cell_line_exp.txt

inst/extdata/mock_5_data_types/cell_line_meth.txt

inst/extdata/mock_5_data_types/cell_line_mut.txt

inst/extdata/mock_5_data_types/cell_line_prot.txt

inst/extdata/mock_5_data_types/default_weights_for_known_cancer_genes_cna.txt

inst/extdata/mock_5_data_types/default_weights_for_known_cancer_genes_exp.txt

inst/extdata/mock_5_data_types/default_weights_for_known_cancer_genes_meth.txt

inst/extdata/mock_5_data_types/default_weights_for_known_cancer_genes_mut.txt

inst/extdata/mock_5_data_types/default_weights_for_known_cancer_genes_prot.txt

inst/extdata/mock_5_data_types/tumor_cna.txt

inst/extdata/mock_5_data_types/tumor_exp.txt

inst/extdata/mock_5_data_types/tumor_meth.txt

inst/extdata/mock_5_data_types/tumor_mut.txt

inst/extdata/mock_5_data_types/tumor_prot.txt

inst/extdata/mtc_results_20200331/mtc_results_20200331.rds

inst/extdata/mtc_results_20200331/mtc_results_20200331_no_factors.rds

inst/extdata/ovarian_tcga_cclp/Genes_and_weights_cna.txt

inst/extdata/ovarian_tcga_cclp/Genes_and_weights_exp.txt

inst/extdata/ovarian_tcga_cclp/Genes_and_weights_mut.txt

inst/extdata/ovarian_tcga_cclp/cell_line_cna.txt

inst/extdata/ovarian_tcga_cclp/cell_line_exp.txt

inst/extdata/ovarian_tcga_cclp/cell_line_mut.txt

inst/extdata/ovarian_tcga_cclp/default_weights_for_known_cancer_genes_cna.txt

inst/extdata/ovarian_tcga_cclp/default_weights_for_known_cancer_genes_exp.txt

inst/extdata/ovarian_tcga_cclp/default_weights_for_known_cancer_genes_mut.txt

inst/extdata/ovarian_tcga_cclp/tumor_cna.txt

inst/extdata/ovarian_tcga_cclp/tumor_exp.txt

inst/extdata/ovarian_tcga_cclp/tumor_mut.txt

inst/extdata/precomputed_geneset_comparisons/precomputed_comparisons.rds

inst/extdata/precomputed_geneset_comparisons/precomputed_comparisons_20211019.rds

inst/extdata/precomputed_geneset_comparisons/selected_geneset_comparisons.rds

inst/extdata/precomputed_geneset_comparisons/selected_geneset_comparisons_20211019.rds

inst/gsoc/mock_dataset_maker.R

inst/ignore/Weighted_similarity_own_measure_quicker.bak

inst/ignore/categorize_cell_lines.bak

inst/ignore/generate_composite_mat_and_gene_weights.bak

inst/ignore/generics.bak

inst/ignore/plot_mds.bak

inst/ignore/run_comparison.bak

inst/pancan_analysis/Read_in_and_prepare.R inst/pancan_analysis/RunTumorComparerExample_updated.R inst/pancan_analysis/RunTumorComparerExample_updated_cont_exp.R inst/pancan_analysis/Run_tumorcomparer_for_multiple_cancer_types.R inst/pancan_analysis/Run_tumorcomparer_for_multiple_cancer_types_cont_exp.R inst/pancan_analysis/Run_tumorcomparer_for_multiple_cancer_types_quantile_normalized.R inst/pancan_analysis/create_binary_mutation_matrix.R inst/pancan_analysis/misc_functions.R inst/pancan_analysis/not_fixed/prepare_cosmic_81_mutations.R inst/pancan_analysis/postprocessing_results.R inst/pancan_analysis/prepare_cosmic_data.R inst/pancan_analysis/prepare_gene_sets.R inst/pancan_analysis/prepare_maf_mutations.R inst/pancan_pathway_analysis/comparison_precalculation.R inst/pancan_pathway_analysis/pancan_pathway_analysis.R inst/scripts/dockerDeploy/README.md

inst/scripts/dockerDeploy/tumorcomparer.json

inst/scripts/dockerDeploy/tumorcomparer.sh

inst/scripts/installPackage.R

inst/scripts/shiny-server.conf

inst/shinyApp/global.R inst/shinyApp/server.R inst/shinyApp/ui.R

inst/shinyApp/www/files/about.html

inst/shinyApp/www/files/about.md

inst/shinyApp/www/js/default_style.js

inst/shinyApp/www/js/google_analytics.js

inst/shinyApp/www/js/nav_append_static.js

inst/shinyApp/www/read_data_for_running_tc.zip

inst/shinyApp/www/read_data_for_running_tc_two_datatypes.zip

inst/shinyApp/www/static/brca_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/brca_cclp_tcga_tumorcomparer_files/figure-html/comparing_breast_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/coad_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/coad_cclp_tcga_tumorcomparer_files/figure-html/comparing_colon_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/esca_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/esca_cclp_tcga_tumorcomparer_files/figure-html/comparing_esophageal_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/google_analytics_static.js

inst/shinyApp/www/static/index.html

inst/shinyApp/www/static/kirc_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/kirc_cclp_tcga_tumorcomparer_files/figure-html/comparing_kidney_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/lihc_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/lihc_cclp_tcga_tumorcomparer_files/figure-html/comparing_liver_hepatocellular_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/luad_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/luad_cclp_tcga_tumorcomparer_files/figure-html/comparing_lung_adenocarcinoma_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/ov_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/ov_cclp_tcga_tumorcomparer_files/figure-html/comparing_ovarian_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/paad_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/paad_cclp_tcga_tumorcomparer_files/figure-html/comparing_pancreatic_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/prad_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css.map

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/bootstrap-theme.min.css

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/bootstrap.css

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/bootstrap.css.map

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/bootstrap.min.css

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/cerulean.min.css

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/cosmo.min.css

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/darkly.min.css

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/flatly.min.css

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/Lato.ttf

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inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/NewsCycle.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/NewsCycleBold.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/OpenSans.ttf

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inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/OpenSansBoldItalic.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/OpenSansItalic.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/OpenSansLight.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/OpenSansLightItalic.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/Raleway.ttf

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inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/RobotoBold.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/RobotoLight.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/RobotoMedium.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/SourceSansPro.ttf

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inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProItalic.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProLight.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/fonts/Ubuntu.ttf

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/journal.min.css

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inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/css/united.min.css

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inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.svg

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.ttf

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inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/js/bootstrap.js

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/js/bootstrap.min.js

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/js/npm.js

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/shim/html5shiv.min.js

inst/shinyApp/www/static/site_libs/bootstrap-3.3.5/shim/respond.min.js

inst/shinyApp/www/static/site_libs/header-attrs-2.13/header-attrs.js

inst/shinyApp/www/static/site_libs/highlightjs-9.12.0/default.css

inst/shinyApp/www/static/site_libs/highlightjs-9.12.0/highlight.js

inst/shinyApp/www/static/site_libs/highlightjs-9.12.0/textmate.css

inst/shinyApp/www/static/site_libs/jquery-3.6.0/jquery-3.6.0.js

inst/shinyApp/www/static/site_libs/jquery-3.6.0/jquery-3.6.0.min.js

inst/shinyApp/www/static/site_libs/jquery-3.6.0/jquery-3.6.0.min.map

inst/shinyApp/www/static/site_libs/kePrint-0.0.1/kePrint.js

inst/shinyApp/www/static/site_libs/navigation-1.1/codefolding.js

inst/shinyApp/www/static/site_libs/navigation-1.1/sourceembed.js

inst/shinyApp/www/static/site_libs/navigation-1.1/tabsets.js

inst/shinyApp/www/static/sitemap.xml

inst/shinyApp/www/static/skcm_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/stad_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/stad_cclp_tcga_tumorcomparer_files/figure-html/comparing_stomach_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/style.css

inst/shinyApp/www/static/thca_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/thca_cclp_tcga_tumorcomparer_files/figure-html/comparing_thyroid_cancer_cell_lines_to_tumor_samples.-1.png

inst/shinyApp/www/static/tumorcomparer_compare_tumor_samples_to_cell_lines_workflow_graphical_abstract.png

inst/shinyApp/www/static/ucec_cclp_tcga_tumorcomparer.html

inst/shinyApp/www/static/ucec_cclp_tcga_tumorcomparer_files/figure-html/comparing_endometrial_cancer_cell_lines_to_tumor_samples.-1.png

inst/static_page_generation/README.md inst/static_page_generation/_session_info.Rmd

inst/static_page_generation/_site.yml

inst/static_page_generation/cbioportal_mutations/mutations_brca.txt

inst/static_page_generation/cbioportal_mutations/mutations_ccle_2019.txt

inst/static_page_generation/cbioportal_mutations/mutations_coad.txt

inst/static_page_generation/cbioportal_mutations/mutations_esca.txt

inst/static_page_generation/cbioportal_mutations/mutations_kirc.txt

inst/static_page_generation/cbioportal_mutations/mutations_lihc.txt

inst/static_page_generation/cbioportal_mutations/mutations_luad.txt

inst/static_page_generation/cbioportal_mutations/mutations_ov.txt

inst/static_page_generation/cbioportal_mutations/mutations_paad.txt

inst/static_page_generation/cbioportal_mutations/mutations_prad.txt

inst/static_page_generation/cbioportal_mutations/mutations_skcm.txt

inst/static_page_generation/cbioportal_mutations/mutations_stad.txt

inst/static_page_generation/cbioportal_mutations/mutations_thca.txt

inst/static_page_generation/cbioportal_mutations/mutations_ucec.txt

inst/static_page_generation/ccle_2019_onco500_PATIENT_DATA_oncoprint.tsv.gz

inst/static_page_generation/ccle_tcga_mapping.txt

inst/static_page_generation/disgenet_tcga_mapping_20220321.txt

inst/static_page_generation/generate_tumorcomparer_static_rmds.R

inst/static_page_generation/google_analytics_static.js

inst/static_page_generation/index.Rmd

inst/static_page_generation/results_citations_binned_20200619.txt

inst/static_page_generation/style.css

inst/static_page_generation/tumorcomparer_compare_tumor_samples_to_cell_lines_workflow_graphical_abstract.png

inst/static_page_generation/tumorcomparer_template.brew

inst/test_output/baloon_plot_result_table.rds

inst/test_output/comparison_2_datasets.rds

inst/test_output/comparison_5_datasets.rds

inst/test_output/comparison_config.rds

inst/test_output/comparison_geneset.rds

inst/test_output/cyj_json_graph.rds

inst/test_output/ov_comparison_result.rds

inst/test_output/ov_composite_mat.rds

man/.Rapp.history

man/ballon_plot_data_to_result_table.Rd man/calc_weighted_corr.Rd man/categorize_cell_lines.Rd man/compute_freq_alt.Rd man/convert_to_0_to_1_using_xminusmin_by_maxminusmin.Rd man/cyj_graph_maker_from_dist_mat.Rd man/generate_composite_mat_and_gene_weights.Rd man/graphNELtoJSON.Rd man/keep_only_high_level_cnas.Rd man/make_balloon_plot_data_from_comparison_result.Rd man/make_balloon_plot_data_from_mtc.Rd man/map_mean_similarity_to_gradient.Rd man/pair_dist.Rd man/plot_balloon_plot.Rd man/plot_joyplot.Rd man/plot_mds.Rd man/return_first_part.Rd man/run_comparison.Rd man/run_comparison_config_list.Rd man/run_shiny_app.Rd man/tc_geneset_comparison.Rd man/tcga_pancan_pathway_genes.Rd man/tic.Rd man/toc.Rd

r-requirements.dcf

tests/testthat.R tests/testthat/test_tumorcomparer.R vignettes/tumorcomparer_example.Rmd

vignettes/tumorcomparer_publication_dataset.bak

cannin/tumorcomparer documentation built on Feb. 7, 2023, 3:13 p.m.