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
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inst/shinyApp/www/static/site_libs/navigation-1.1/tabsets.js
inst/shinyApp/www/static/sitemap.xml
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inst/shinyApp/www/static/stad_cclp_tcga_tumorcomparer.html
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inst/shinyApp/www/static/style.css
inst/shinyApp/www/static/thca_cclp_tcga_tumorcomparer.html
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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
