Files in UCSCXenaShiny

Interactive Analysis of UCSC Xena Data

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

R/globalVariables.R R/GeomSplitViolin.R R/vis_identifier.R R/query_custom_value.R R/vis_toil_Mut.R R/ezcor.R R/vis_pcawg_value.R R/utils-pipe.R R/ccle.R R/vis_identifier_dim_dist.R R/data.R R/query_toil_value_df.R R/xenashiny.R R/load_data.R R/tcga_surv.R R/analyze_gene_drug_response.R R/query_value.R R/query_tcga_group.R R/vis_dim_dist.R R/run.R R/vis_analyze_gene_drug_response.R R/get_pancan_value.R R/zzz.R R/vis_gene_pw_cor.R R/ope_pancan_value.R R/get_pcawg_value.R R/vis_pancan_value.R R/vis_ccle_value.R R/query_general.R R/utils.R inst/doc/api.Rmd inst/doc/api.R

inst/doc/api.html

inst/modules_apps/app.R inst/modules_apps/xx_modules.R inst/modules_apps/simple_module_from_rstudio.R inst/shinyapp/PGdata.R inst/shinyapp/App.R inst/shinyapp/utils_plot.R inst/shinyapp/utils_appdata.R inst/shinyapp/utils_pkgs.R inst/shinyapp/utils_func.R

inst/shinyapp/www/file.png

inst/shinyapp/www/xena_shiny-logo_white.png

inst/shinyapp/www/host.png

inst/shinyapp/www/20210708184045.png

inst/shinyapp/www/site.png

inst/shinyapp/www/sample.png

inst/shinyapp/www/bootstrap4.css

inst/shinyapp/www/chooser-binding.js

inst/shinyapp/www/xena_shiny-logo.png

inst/shinyapp/www/cohort.png

inst/shinyapp/www/dataset.png

inst/shinyapp/www/slick_img/N5.png

inst/shinyapp/www/slick_img/N6.png

inst/shinyapp/www/slick_img/N2.png

inst/shinyapp/www/slick_img/N3.png

inst/shinyapp/www/slick_img/N4.png

inst/shinyapp/www/slick_img/N1.png

inst/shinyapp/www/js/bootstrap.js

inst/shinyapp/www/js/bootstrap.min.js.map

inst/shinyapp/www/js/bootstrap.bundle.js

inst/shinyapp/www/js/bootstrap.bundle.min.js

inst/shinyapp/www/js/bootstrap.js.map

inst/shinyapp/www/js/bootstrap.bundle.min.js.map

inst/shinyapp/www/js/bootstrap.bundle.js.map

inst/shinyapp/www/js/bootstrap.min.js

inst/shinyapp/www/css/global.css

inst/shinyapp/www/css/bootstrap.min.css.map

inst/shinyapp/www/css/bootstrap-grid.css

inst/shinyapp/www/css/bootstrap-reboot.css

inst/shinyapp/www/css/bootstrap.css

inst/shinyapp/www/css/bootstrap-reboot.css.map

inst/shinyapp/www/css/bootstrap.css.map

inst/shinyapp/www/css/bootstrap-grid.min.css.map

inst/shinyapp/www/css/bootstrap-grid.css.map

inst/shinyapp/www/css/bootstrap-reboot.min.css

inst/shinyapp/www/css/bootstrap.min.css

inst/shinyapp/www/css/bootstrap-grid.min.css

inst/shinyapp/www/css/bootstrap-reboot.min.css.map

inst/shinyapp/shiny-doc/intro_quick_mods.md inst/shinyapp/shiny-doc/usage.md inst/shinyapp/shiny-doc/intro_personal_pips.md inst/shinyapp/shiny-doc/datasets.md inst/shinyapp/shiny-doc/citation.md inst/shinyapp/shiny-doc/terms.md inst/shinyapp/shiny-doc/tmp.md inst/shinyapp/shiny-doc/citation2.md inst/shinyapp/modules/02_quick/modules-1-tcga-07-PW.R inst/shinyapp/modules/02_quick/modules-2-pcawg-01-TN.R inst/shinyapp/modules/02_quick/modules-1-tcga-11-Dim.R inst/shinyapp/modules/02_quick/modules-1-tcga-09-KM.R inst/shinyapp/modules/02_quick/modules-1-tcga-04-TIL.R inst/shinyapp/modules/02_quick/modules-1-tcga-06-Idx.R inst/shinyapp/modules/02_quick/modules-3-ccle-01-Dist.R inst/shinyapp/modules/02_quick/modules-1-tcga-10-Cox.R inst/shinyapp/modules/02_quick/modules-1-tcga-01-TN.R inst/shinyapp/modules/02_quick/modules-2-pcawg-03-KM.R inst/shinyapp/modules/02_quick/modules-1-tcga-03-Cor.R inst/shinyapp/modules/02_quick/modules-2-pcawg-02-Cor.R inst/shinyapp/modules/02_quick/modules-3-ccle-04-DrugR.R inst/shinyapp/modules/02_quick/modules-1-tcga-08-Mut.R inst/shinyapp/modules/02_quick/modules-1-tcga-05-Immune.R inst/shinyapp/modules/02_quick/modules-1-tcga-02-Anatomy.R inst/shinyapp/modules/02_quick/modules-2-pcawg-04-Cox.R inst/shinyapp/modules/02_quick/modules-z-quick-mol-select.R inst/shinyapp/modules/02_quick/modules-3-ccle-02-Cor.R inst/shinyapp/modules/02_quick/modules-3-ccle-03-DrugT.R inst/shinyapp/modules/08_other_page/modules-z-download-2-dataset.R inst/shinyapp/modules/08_other_page/modules-z-download-1-pancan.R inst/shinyapp/modules/08_other_page/modules-file-upload.R inst/shinyapp/modules/08_other_page/home-daily-gene.R inst/shinyapp/modules/08_other_page/modules-z-help-id.R inst/shinyapp/modules/08_other_page/home-pancan-search.R inst/shinyapp/modules/08_other_page/combo-single-gene-pan-cancer-analysis.R inst/shinyapp/modules/04_pcawg/modules-pcawg-cor-m2o.R inst/shinyapp/modules/04_pcawg/modules-pcawg-sur-o2m.R inst/shinyapp/modules/04_pcawg/modules-pcawg-sur-o2o.R inst/shinyapp/modules/04_pcawg/modules-pcawg-cor-o2m.R inst/shinyapp/modules/04_pcawg/modules-pcawg-comp-o2o.R inst/shinyapp/modules/04_pcawg/modules-pcawg-cor-o2o.R inst/shinyapp/modules/04_pcawg/modules-pcawg-comp-m2o.R inst/shinyapp/modules/04_pcawg/modules-pcawg-sur-m2o.R inst/shinyapp/modules/04_pcawg/modules-pcawg-comp-o2m.R inst/shinyapp/modules/07_PharmacoGenomics/DrugOmicPair.R inst/shinyapp/modules/07_PharmacoGenomics/FeatureAcrossType.R inst/shinyapp/modules/07_PharmacoGenomics/ProfileDrugSens.R inst/shinyapp/modules/07_PharmacoGenomics/StatAnno.R inst/shinyapp/modules/07_PharmacoGenomics/FeatureDatabaseSig_singlethread.R inst/shinyapp/modules/06_tpc_func/modules-z-custom-meta.R inst/shinyapp/modules/06_tpc_func/modules-z-filter-sample.R inst/shinyapp/modules/06_tpc_func/modules-z-download-feat.R inst/shinyapp/modules/06_tpc_func/modules-z-download-res.R inst/shinyapp/modules/06_tpc_func/modules-z-add-signature.R inst/shinyapp/modules/06_tpc_func/modules-z-group-sample.R inst/shinyapp/modules/06_tpc_func/modules-z-mol-origin.R inst/shinyapp/modules/06_tpc_func/modules-z-multi-upload.R inst/shinyapp/modules/03_tcga/modules-pancan-comp-o2o.R inst/shinyapp/modules/03_tcga/modules-pancan-sur-o2o.R inst/shinyapp/modules/03_tcga/modules-pancan-cor-o2o.R inst/shinyapp/modules/03_tcga/modules-pancan-cor-o2m.R inst/shinyapp/modules/03_tcga/modules-pancan-sur-o2m.R inst/shinyapp/modules/03_tcga/modules-pancan-cor-m2o.R inst/shinyapp/modules/03_tcga/modules-pancan-sur-m2o.R inst/shinyapp/modules/03_tcga/modules-pancan-comp-m2o.R inst/shinyapp/modules/03_tcga/modules-pancan-comp-o2m.R inst/shinyapp/modules/05_ccle/modules-ccle-cor-m2o.R inst/shinyapp/modules/05_ccle/modules-ccle-cor-o2o.R inst/shinyapp/modules/05_ccle/modules-ccle-comp-o2o.R inst/shinyapp/modules/05_ccle/modules-ccle-comp-m2o.R inst/shinyapp/modules/01_general/modules-ga-surv-analysis.R inst/shinyapp/modules/01_general/modules-ga-matrix-correlation.R inst/shinyapp/modules/01_general/modules-ga-scatter-correlation.R inst/shinyapp/modules/01_general/modules-ga-dim-distribution.R inst/shinyapp/modules/01_general/modules-ga-group-comparison.R inst/shinyapp/ui/pancan-analysis-quick.R inst/shinyapp/ui/repository.R inst/shinyapp/ui/home.R inst/shinyapp/ui/general-analysis.R inst/shinyapp/ui/footer.R inst/shinyapp/ui/global.R inst/shinyapp/ui/developers.R inst/shinyapp/ui/help.R inst/shinyapp/ui/pancan-download.R inst/shinyapp/ui/chooser.R inst/shinyapp/ui/pancan-analysis-tpc.R inst/shinyapp/ui/PharmacoGenomics.R inst/shinyapp/server/repository.R inst/shinyapp/server/home.R inst/shinyapp/server/general-analysis.R inst/shinyapp/server/modules.R inst/shinyapp/server/global.R inst/shinyapp/helper/get_batch_data_set_groups.md inst/shinyapp/helper/home_query.md inst/shinyapp/helper/data_origin.md inst/shinyapp/helper/custom_metadata.md inst/shinyapp/helper/set_groups.md inst/shinyapp/helper/analyze_cor_1.md inst/shinyapp/helper/choose_samples.md inst/shinyapp/helper/sur_initial_group.md inst/shinyapp/helper/analyze_sur_2.md inst/shinyapp/helper/analyze_comp_2.md inst/shinyapp/helper/tcga_types.md inst/shinyapp/helper/pcawg_projects.md inst/shinyapp/helper/analyze_cor_2.md inst/shinyapp/helper/analyze_sur_3.md inst/shinyapp/helper/get_batch_data.md inst/shinyapp/helper/get_one_data.md inst/shinyapp/helper/batch_ids.md inst/shinyapp/helper/analyze_sur_1.md inst/shinyapp/helper/analyze_cor_3.md inst/shinyapp/helper/add_signature.md inst/shinyapp/helper/analyze_comp_1.md inst/shinyapp/helper/analyze_comp_3.md

inst/extdata/XenaInfo.RData

inst/rmd/report_template.Rmd

build/vignette.rds

tests/testthat.R tests/testthat/test-vis_pancan_value.R tests/testthat/test-run_app.R vignettes/api.Rmd

data/tcga_genome_instability.rda

data/ccle_info.rda

data/tcga_clinical_fine.rda

data/pcawg_info.rda

data/TCGA.organ.rda

data/ccle_info_fine.rda

data/toil_info.rda

data/tcga_clinical.rda

data/tcga_purity.rda

data/ccle_absolute.rda

data/tcga_surv.rda

data/pcawg_info_fine.rda

data/tcga_gtex.rda

data/pcawg_purity.rda

data/tcga_subtypes.rda

man/vis_pcawg_unicox_tree.Rd man/pcawg_purity.Rd man/vis_gene_cor_cancer.Rd man/ezcor.Rd man/pcawg_info_fine.Rd man/keep_cat_cols.Rd man/tcga_subtypes.Rd man/available_hosts.Rd man/query_general_value.Rd man/pcawg_info.Rd man/vis_unicox_tree.Rd man/vis_identifier_dim_dist.Rd man/app_run.Rd man/vis_gene_TIL_cor.Rd man/vis_toil_TvsN.Rd man/vis_gene_drug_response_asso.Rd man/vis_gene_pw_cor.Rd man/load_data.Rd man/ezcor_partial_cor.Rd man/query_tcga_group.Rd man/vis_gene_cor.Rd man/vis_identifier_cor.Rd man/UCSCXenaShiny-package.Rd man/query_molecule_value.Rd man/vis_toil_Mut_cancer.Rd man/vis_gene_tmb_cor.Rd man/toil_info.Rd man/vis_toil_TvsN_cancer.Rd man/vis_pcawg_dist.Rd man/dot-opt_pancan.Rd man/mol_quick_analysis.Rd man/get_pancan_value.Rd man/analyze_gene_drug_response_diff.Rd man/vis_toil_Mut.Rd man/vis_identifier_grp_comparison.Rd man/ezcor_batch.Rd man/vis_ccle_tpm.Rd man/vis_identifier_multi_cor.Rd man/analyze_gene_drug_response_asso.Rd man/vis_gene_stemness_cor.Rd man/query_toil_value_df.Rd man/pipe.Rd man/vis_gene_msi_cor.Rd man/ccle_absolute.Rd man/tcga_purity.Rd man/ccle_info_fine.Rd man/tcga_surv.Rd man/tcga_clinical_fine.Rd man/tcga_gtex.Rd man/vis_identifier_grp_surv.Rd man/ccle_info.Rd man/vis_dim_dist.Rd man/tcga_surv_analysis.Rd man/query_pancan_value.Rd man/tcga_tmb.Rd man/tcga_clinical.Rd man/vis_gene_immune_cor.Rd man/vis_gene_drug_response_diff.Rd man/vis_pancan_anatomy.Rd man/tcga_genome_instability.Rd man/vis_ccle_gene_cor.Rd man/vis_pcawg_gene_cor.Rd man/TCGA.organ.Rd

UCSCXenaShiny documentation built on May 29, 2024, 1:10 a.m.