├── .Rbuildignore ├── .dockerignore ├── .github ├── .gitignore ├── CONTRIBUTING.md └── workflows │ ├── autobuilds.yml │ ├── pkgdown.yaml │ └── r-check.yml ├── .gitignore ├── CRAN-RELEASE ├── CRAN-SUBMISSION ├── DESCRIPTION ├── Dockerfile ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── GeomSplitViolin.R ├── analyze_gene_drug_response.R ├── ccle.R ├── data.R ├── ezcor.R ├── get_nonomics_value.R ├── get_pancan_value.R ├── get_pcawg_value.R ├── globalVariables.R ├── load_data.R ├── ope_pancan_value.R ├── query_custom_value.R ├── query_general.R ├── query_tcga_group.R ├── query_toil_value_df.R ├── query_value.R ├── run.R ├── tcga_surv.R ├── utils-pipe.R ├── utils.R ├── vis_analyze_gene_drug_response.R ├── vis_ccle_value.R ├── vis_cross.R ├── vis_dim_dist.R ├── vis_gene_pw_cor.R ├── vis_identifier.R ├── vis_identifier_dim_dist.R ├── vis_pancan_value.R ├── vis_pcawg_value.R ├── vis_toil_Mut.R ├── xenashiny.R └── zzz.R ├── README.md ├── XenaShiny.Rproj ├── _pkgdown.yml ├── codecov.yml ├── data-raw ├── app_history.R ├── calc_TIL_PW.R ├── ccle_drugs.R ├── clean_promoter_id.R ├── function │ ├── id_reference.R │ ├── my_functions.r │ └── pcor.r ├── pancan_identifier_help.R ├── query_pcawg_data.R ├── raw-data-collection-and-tidying.R ├── tcga_clinical_fine_etc.R ├── update_tcga_cli.R └── v2_TPC_id_value.r ├── data-remote ├── pancan_MSI.rda ├── tcga_MSI.rda ├── tcga_TIL.rda ├── tcga_chr_alteration.rda ├── tcga_pan_immune_signature.rda ├── tcga_stemness.rda └── tcga_tmb.rda ├── data ├── TCGA.organ.rda ├── ccle_absolute.rda ├── ccle_info.rda ├── ccle_info_fine.rda ├── pcawg_info.rda ├── pcawg_info_fine.rda ├── pcawg_purity.rda ├── tcga_clinical.rda ├── tcga_clinical_fine.rda ├── tcga_genome_instability.rda ├── tcga_gtex.rda ├── tcga_purity.rda ├── tcga_subtypes.rda ├── tcga_surv.rda └── toil_info.rda ├── deploy.R ├── deploy.html ├── deploy_basic.R ├── inst ├── extdata │ └── XenaInfo.RData ├── modules_apps │ ├── app.R │ ├── simple_module_from_rstudio.R │ └── xx_modules.R ├── rmd │ └── report_template.Rmd └── shinyapp │ ├── App.R │ ├── PGdata.R │ ├── app_preset.R │ ├── helper │ ├── add_signature.md │ ├── analyze_comp_1.md │ ├── analyze_comp_2.md │ ├── analyze_comp_3.md │ ├── analyze_cor_1.md │ ├── analyze_cor_2.md │ ├── analyze_cor_3.md │ ├── analyze_sur_1.md │ ├── analyze_sur_2.md │ ├── analyze_sur_3.md │ ├── choose_samples.md │ ├── cross_gene.md │ ├── cross_pw.md │ ├── custom_metadata.md │ ├── data_origin.md │ ├── get_batch_data.md │ ├── get_batch_data_set_groups.md │ ├── get_one_data.md │ ├── pcawg_projects.md │ ├── set_groups.md │ └── tcga_types.md │ ├── modules │ ├── 01_general │ │ ├── modules-ga-dim-distribution.R │ │ ├── modules-ga-group-comparison.R │ │ ├── modules-ga-matrix-correlation.R │ │ ├── modules-ga-scatter-correlation.R │ │ └── modules-ga-surv-analysis.R │ ├── 02_quick │ │ ├── modules-1-tcga-01-TN.R │ │ ├── modules-1-tcga-02-Anatomy.R │ │ ├── modules-1-tcga-03-Cor.R │ │ ├── modules-1-tcga-04-TIL.R │ │ ├── modules-1-tcga-05-Immune.R │ │ ├── modules-1-tcga-06-Idx.R │ │ ├── modules-1-tcga-07-PW.R │ │ ├── modules-1-tcga-08-Mut.R │ │ ├── modules-1-tcga-09-KM.R │ │ ├── modules-1-tcga-10-Cox.R │ │ ├── modules-1-tcga-11-Dim.R │ │ ├── modules-2-pcawg-01-TN.R │ │ ├── modules-2-pcawg-02-Cor.R │ │ ├── modules-2-pcawg-03-KM.R │ │ ├── modules-2-pcawg-04-Cox.R │ │ ├── modules-3-ccle-01-Dist.R │ │ ├── modules-3-ccle-02-Cor.R │ │ ├── modules-3-ccle-03-DrugT.R │ │ ├── modules-3-ccle-04-DrugR.R │ │ └── modules-z-quick-mol-select.R │ ├── 03_tcga │ │ ├── modules-pancan-comp-m2o.R │ │ ├── modules-pancan-comp-o2m.R │ │ ├── modules-pancan-comp-o2o.R │ │ ├── modules-pancan-cor-m2o.R │ │ ├── modules-pancan-cor-o2m.R │ │ ├── modules-pancan-cor-o2o.R │ │ ├── modules-pancan-cross-gene-o2m.R │ │ ├── modules-pancan-cross-pw-o2m.R │ │ ├── modules-pancan-sur-m2o.R │ │ ├── modules-pancan-sur-o2m.R │ │ └── modules-pancan-sur-o2o.R │ ├── 04_pcawg │ │ ├── modules-pcawg-comp-m2o.R │ │ ├── modules-pcawg-comp-o2m.R │ │ ├── modules-pcawg-comp-o2o.R │ │ ├── modules-pcawg-cor-m2o.R │ │ ├── modules-pcawg-cor-o2m.R │ │ ├── modules-pcawg-cor-o2o.R │ │ ├── modules-pcawg-sur-m2o.R │ │ ├── modules-pcawg-sur-o2m.R │ │ └── modules-pcawg-sur-o2o.R │ ├── 05_ccle │ │ ├── modules-ccle-comp-m2o.R │ │ ├── modules-ccle-comp-o2o.R │ │ ├── modules-ccle-cor-m2o.R │ │ └── modules-ccle-cor-o2o.R │ ├── 06_tpc_func │ │ ├── modules-z-add-signature.R │ │ ├── modules-z-custom-meta.R │ │ ├── modules-z-download-feat.R │ │ ├── modules-z-download-res.R │ │ ├── modules-z-filter-sample.R │ │ ├── modules-z-group-sample.R │ │ ├── modules-z-mol-origin.R │ │ └── modules-z-multi-upload.R │ ├── 07_PharmacoGenomics │ │ ├── DrugOmicPair.R │ │ ├── FeatureAcrossType.R │ │ ├── FeatureDatabaseSig_singlethread.R │ │ ├── ProfileDrugSens.R │ │ └── StatAnno.R │ └── 08_other_page │ │ ├── combo-single-gene-pan-cancer-analysis.R │ │ ├── home-daily-gene.R │ │ ├── home-pancan-search.R │ │ ├── modules-file-upload.R │ │ ├── modules-z-download-1-pancan.R │ │ ├── modules-z-download-2-dataset.R │ │ └── modules-z-help-id.R │ ├── server │ ├── general-analysis.R │ ├── global.R │ ├── home.R │ ├── modules.R │ └── repository.R │ ├── shiny-doc │ ├── citation.md │ ├── citation2.md │ ├── datasets.md │ ├── intro_personal_pips.md │ ├── intro_quick_mods.md │ ├── terms.md │ ├── tmp.md │ └── usage.md │ ├── ui │ ├── PharmacoGenomics.R │ ├── chooser.R │ ├── developers.R │ ├── footer.R │ ├── general-analysis.R │ ├── global.R │ ├── help.R │ ├── home.R │ ├── link2advanced.R │ ├── pancan-analysis-quick.R │ ├── pancan-analysis-tpc.R │ ├── pancan-download.R │ └── repository.R │ ├── utils_appdata.R │ ├── utils_func.R │ ├── utils_pkgs.R │ ├── utils_plot.R │ └── www │ ├── 20210708184045.png │ ├── Quick_guide.pdf │ ├── bootstrap4.css │ ├── chooser-binding.js │ ├── cohort.png │ ├── css │ ├── bootstrap-grid.css │ ├── bootstrap-grid.css.map │ ├── bootstrap-grid.min.css │ ├── bootstrap-grid.min.css.map │ ├── bootstrap-reboot.css │ ├── bootstrap-reboot.css.map │ ├── bootstrap-reboot.min.css │ ├── bootstrap-reboot.min.css.map │ ├── bootstrap.css │ ├── bootstrap.css.map │ ├── bootstrap.min.css │ ├── bootstrap.min.css.map │ └── global.css │ ├── dataset.png │ ├── file.png │ ├── host.png │ ├── icon.png │ ├── js │ ├── bootstrap.bundle.js │ ├── bootstrap.bundle.js.map │ ├── bootstrap.bundle.min.js │ ├── bootstrap.bundle.min.js.map │ ├── bootstrap.js │ ├── bootstrap.js.map │ ├── bootstrap.min.js │ └── bootstrap.min.js.map │ ├── sample.png │ ├── site.png │ ├── slick_img │ ├── N1.png │ ├── N2.png │ ├── N3.png │ ├── N4.png │ ├── N5.png │ └── N6.png │ ├── xena_shiny-logo.png │ └── xena_shiny-logo_white.png ├── man ├── TCGA.organ.Rd ├── UCSCXenaShiny-package.Rd ├── analyze_gene_drug_response_asso.Rd ├── analyze_gene_drug_response_diff.Rd ├── app_run.Rd ├── app_run2.Rd ├── available_hosts.Rd ├── calc_pw_mut_cnv.Rd ├── ccle_absolute.Rd ├── ccle_info.Rd ├── ccle_info_fine.Rd ├── dot-opt_pancan.Rd ├── ezcor.Rd ├── ezcor_batch.Rd ├── ezcor_partial_cor.Rd ├── get_nonomics_value.Rd ├── get_pancan_value.Rd ├── keep_cat_cols.Rd ├── load_data.Rd ├── mol_quick_analysis.Rd ├── pcawg_info.Rd ├── pcawg_info_fine.Rd ├── pcawg_purity.Rd ├── pipe.Rd ├── query_general_value.Rd ├── query_molecule_value.Rd ├── query_pancan_value.Rd ├── query_tcga_group.Rd ├── query_toil_value_df.Rd ├── tcga_clinical.Rd ├── tcga_clinical_fine.Rd ├── tcga_genome_instability.Rd ├── tcga_gtex.Rd ├── tcga_purity.Rd ├── tcga_subtypes.Rd ├── tcga_surv.Rd ├── tcga_surv_analysis.Rd ├── tcga_tmb.Rd ├── toil_info.Rd ├── vis_ccle_gene_cor.Rd ├── vis_ccle_tpm.Rd ├── vis_dim_dist.Rd ├── vis_gene_TIL_cor.Rd ├── vis_gene_cor.Rd ├── vis_gene_cor_cancer.Rd ├── vis_gene_cross_omics.Rd ├── vis_gene_drug_response_asso.Rd ├── vis_gene_drug_response_diff.Rd ├── vis_gene_immune_cor.Rd ├── vis_gene_msi_cor.Rd ├── vis_gene_pw_cor.Rd ├── vis_gene_stemness_cor.Rd ├── vis_gene_tmb_cor.Rd ├── vis_identifier_cor.Rd ├── vis_identifier_dim_dist.Rd ├── vis_identifier_grp_comparison.Rd ├── vis_identifier_grp_surv.Rd ├── 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