├── .Rbuildignore ├── .dockerignore ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── Dockerfile ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── app_config.R ├── app_server.R ├── app_ui.R ├── data.R ├── fct_annotation.R ├── fct_cluster_verse.R ├── fct_function_verse.R ├── fct_gene_verse.R ├── fct_int_pair_modules.R ├── fct_multi_cond.R ├── fct_upload.R ├── fct_upload_custom.R ├── golem_utils_server.R ├── golem_utils_ui.R ├── mod_about.R ├── mod_cluster_verse.R ├── mod_function_verse.R ├── mod_gene_verse.R ├── mod_int_pair_modules.R ├── mod_multi_cond.R ├── mod_table_view.R ├── mod_upload.R ├── mod_upload_custom.R ├── run_app.R ├── sysdata.rda └── utils_upload.R ├── README.Rmd ├── README.md ├── data-raw ├── input_data.R └── internal_data.R ├── data └── input.data.rda ├── dev ├── 01_start.R ├── 02_dev.R ├── 03_deploy.R └── run_dev.R ├── inst ├── app │ ├── extdata │ │ ├── cpdb_complex_input.csv │ │ ├── cpdb_gene_input.csv │ │ └── custom_input.csv │ └── www │ │ ├── About_shiny_lowres.png │ │ ├── logoShiny.png │ │ └── logo_lowres.png └── golem-config.yml ├── man ├── annotateGO.Rd ├── annotatePathways.Rd ├── buildPairsbyFunctionMatrix.Rd ├── checkLL_RR.Rd ├── circlePlot.Rd ├── combineAnnotations.Rd ├── createBarPlot1_ggplot.Rd ├── createBarPlot2_CV.Rd ├── createBarPlot2_ggplot.Rd ├── createBarPlot_CV.Rd ├── createNetwork.Rd ├── dendroIntPairModules.Rd ├── elbowPoint.Rd ├── ensemblLink.Rd ├── getBack2BackBarplot.Rd ├── getBarplotDF.Rd ├── getBarplotDF2.Rd ├── getClusterA_Names.Rd ├── getClusterColors.Rd ├── getClusterNames.Rd ├── getClusterNetwork.Rd ├── getClusterSize.Rd ├── getDistinctCouplets.Rd ├── getDotPlot_selInt.Rd ├── getGObiomaRt.Rd ├── getGeneTable.Rd ├── getHitsf.Rd ├── getIntFlow.Rd ├── getNtermsBYdb.Rd ├── getNumLR.Rd ├── getPieChart.Rd ├── getRadar_df.Rd ├── getRankedTerms.Rd ├── getSignif_table.Rd ├── getSignificantFunctions.Rd ├── getSignificantFunctions_multiCond.Rd ├── getSunburst.Rd ├── getUMAPipModules.Rd ├── getUniqueDotplot.Rd 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