Files in CRI-iAtlas/iatlas-app

What the Package Does (One Line, Title Case)

LICENSE.md R/barplot.R R/boxplot.R R/call_iatlas_module.R R/call_module_server.R R/cellimage_functions.R R/cellimage_main_server.R R/cellimage_main_ui.R R/cellimage_network_server.R R/cellimage_network_ui.R R/cellimage_plot_server.R R/cellimage_plot_ui.R R/cellimage_server.R R/cellimage_ui.R R/clinical_outcomes_functions.R R/clinical_outcomes_heatmap_server.R R/clinical_outcomes_heatmap_ui.R R/clinical_outcomes_server.R R/clinical_outcomes_survival_server.R R/clinical_outcomes_survival_ui.R R/clinical_outcomes_ui.R R/copy_number_functions.R R/copy_number_response_server.R R/copy_number_response_ui.R R/copy_number_server.R R/copy_number_ui.R R/data_info_functions.R R/data_info_server.R R/data_info_ui.R R/data_table_server.R R/data_table_ui.R R/docspage.R R/driver_associations_server.R R/driver_associations_ui.R R/explorepage.R R/extracellular_network_functions.R R/extracellular_network_main_server.R R/extracellular_network_main_ui.R R/extracellular_network_server.R R/extracellular_network_ui.R R/forestplot.R R/format.R R/germline_functions.R R/germline_gwas_server.R R/germline_gwas_ui.R R/germline_heritability_server.R R/germline_heritability_ui.R R/germline_rarevariants_server.R R/germline_rarevariants_ui.R R/germline_server.R R/germline_ui.R R/global.R R/globals.R R/heatmap.R R/histogram.R R/ici_clinical_outcomes_functions.R R/ici_clinical_outcomes_plot_server.R R/ici_clinical_outcomes_plot_ui.R R/ici_clinical_outcomes_server.R R/ici_clinical_outcomes_ui.R R/ici_distribution_functions.R R/ici_distribution_server.R R/ici_distribution_ui.R R/ici_hazard_ratio_functions.R R/ici_hazard_ratio_main_server.R R/ici_hazard_ratio_main_ui.R R/ici_hazard_ratio_server.R R/ici_hazard_ratio_ui.R R/ici_immune_features_server.R R/ici_immune_features_ui.R R/ici_immunomodulators_server.R R/ici_immunomodulators_ui.R R/ici_load_data.R R/ici_models_main_server.R R/ici_models_main_ui.R R/ici_models_server.R R/ici_models_train_functions.R R/ici_models_train_server.R R/ici_models_train_ui.R R/ici_models_ui.R R/ici_modules_functions.R R/ici_neoantigen_classes_server.R R/ici_neoantigen_classes_ui.R R/ici_neoantigen_correlations_server.R R/ici_neoantigen_correlations_ui.R R/ici_neoantigen_frequency_server.R R/ici_neoantigen_frequency_ui.R R/ici_neoantigen_server.R R/ici_neoantigen_ui.R R/ici_overview_category_server.R R/ici_overview_category_ui.R R/ici_overview_datasets_server.R R/ici_overview_datasets_ui.R R/ici_overview_functions.R R/ici_overview_server.R R/ici_overview_ui.R R/immune_feature_correlations_server.R R/immune_feature_correlations_ui.R R/immune_feature_distributions_server.R R/immune_feature_distributions_ui.R R/immune_features_server.R R/immune_features_ui.R R/immune_subtype_classifier_functions.R R/immune_subtype_classifier_server.R R/immune_subtype_classifier_ui.R R/immunomodulator_datatable_server.R R/immunomodulator_datatable_ui.R R/immunomodulator_distributions_server.R R/immunomodulator_distributions_ui.R R/immunomodulators_functions.R R/immunomodulators_server.R R/immunomodulators_ui.R R/io_target_datatable_server.R R/io_target_datatable_ui.R R/io_target_distributions_server.R R/io_target_distributions_ui.R R/io_target_functions.R R/io_targets_server.R R/io_targets_ui.R R/kmplot.R R/model_selection_functions.R R/model_selection_server.R R/model_selection_ui.R R/module_ui.R R/sc_bubbleplot_server.R R/sc_bubbleplot_ui.R R/sc_immune_features_distribution_server.R R/sc_immune_features_distribution_ui.R R/sc_immune_features_server.R R/sc_immune_features_ui.R R/sc_immunomodulators_server.R R/sc_immunomodulators_ui.R R/sc_umap_server.R R/sc_umap_ui.R R/scatterplot.R R/til_map_datatable_functions.R R/til_map_datatable_server.R R/til_map_datatable_ui.R R/til_map_distributions_server.R R/til_map_distributions_ui.R R/til_map_server.R R/til_map_ui.R R/tumor_microenvironment_cell_proportions_server.R R/tumor_microenvironment_cell_proportions_ui.R R/tumor_microenvironment_server.R R/tumor_microenvironment_type_fractions_server.R R/tumor_microenvironment_type_fractions_ui.R R/tumor_microenvironment_ui.R R/utils.R R/violinplot.R README.md init.R inst/markdown/about.markdown inst/markdown/cell_type_fractions.markdown inst/markdown/cellimage.markdown inst/markdown/clinical_outcomes.markdown inst/markdown/clinical_outcomes_heatmap.markdown inst/markdown/clinical_outcomes_survival.markdown inst/markdown/cohort_dataset_selection.markdown inst/markdown/cohort_filter_selection.markdown inst/markdown/cohort_group_selection.markdown inst/markdown/cohort_selection1.markdown inst/markdown/cohort_selection2.markdown inst/markdown/cox_regression.markdown inst/markdown/data_info.markdown inst/markdown/data_info_readouts.markdown inst/markdown/docs.markdown inst/markdown/driver.markdown inst/markdown/driver_multi.markdown inst/markdown/driver_single.markdown inst/markdown/explore1.markdown inst/markdown/explore2.markdown inst/markdown/explore3.markdown inst/markdown/explore4.markdown inst/markdown/extracellular_network.markdown inst/markdown/extracellular_network_main.markdown inst/markdown/germline_gwas.markdown inst/markdown/germline_heritability.markdown inst/markdown/ici_clinical_outcomes.markdown inst/markdown/ici_hazard_ratio.markdown inst/markdown/ici_immunefeatures.markdown inst/markdown/ici_immunomodulators.markdown inst/markdown/ici_models.markdown inst/markdown/ici_overview_datasets.markdown inst/markdown/immune_features_correlations.markdown inst/markdown/immune_features_dist.markdown inst/markdown/immunomodulators.markdown inst/markdown/immunomodulators_distributions.markdown inst/markdown/immunomodulators_dt.markdown inst/markdown/io_target.markdown inst/markdown/io_target_dist.markdown inst/markdown/io_target_dt.markdown inst/markdown/methods/BCR.markdown inst/markdown/methods/CI.markdown inst/markdown/methods/CIBERSORT.markdown inst/markdown/methods/CNVR-DDR.markdown inst/markdown/methods/CellImage_method.markdown inst/markdown/methods/ExpSig.markdown inst/markdown/methods/LENS_Neoantigen.markdown inst/markdown/methods/LF.markdown inst/markdown/methods/Response_ICI_Predictors.markdown inst/markdown/methods/Survival.markdown inst/markdown/methods/TCGASubtype.markdown inst/markdown/methods/TCR.markdown inst/markdown/methods/germline-colocalization.md inst/markdown/methods/germline-gwas.md inst/markdown/methods/germline-rarevariants.md inst/markdown/methods/germline_heritability.md inst/markdown/methods/ici_models.markdown inst/markdown/methods/neoantigen-classes.markdown inst/markdown/methods/neoantigen-correlation.markdown inst/markdown/methods/neoantigen-frequency.markdown inst/markdown/methods/neoantigen-prediction.markdown inst/markdown/methods/pMHC-Indel.markdown inst/markdown/methods/pMHC-SNV.markdown inst/markdown/methods/sc-pseudobulk-scoring.md inst/markdown/methods/sc-pseudobulk.md inst/markdown/notebook.markdown inst/markdown/overall_cell_proportions1.markdown inst/markdown/overall_cell_proportions2.markdown inst/markdown/resources.markdown inst/markdown/sample_groups_overlap.markdown inst/markdown/sc_immunefeatures.markdown inst/markdown/sc_immunomodulators.markdown inst/markdown/sc_immunomodulators_bubbleplot.markdown inst/markdown/tilmap.markdown inst/markdown/tilmap_dist.markdown inst/markdown/tilmap_table.markdown inst/markdown/tumor_microenvironment.markdown install_and_init.R man/create_heritability_df.Rd man/create_tm_slide_link.Rd man/filter_feature_tbl.Rd man/format_feature_tbl.Rd man/format_filtered_feature_tbl.Rd renv/activate.R server.R tests/testthat.R tests/testthat/helper-globals.R tests/testthat/test-call_module_server.R tests/testthat/test-cellimage_functions.R tests/testthat/test-cellimage_main_server.R tests/testthat/test-cellimage_main_ui.R tests/testthat/test-cellimage_network_server.R tests/testthat/test-cellimage_network_ui.R tests/testthat/test-cellimage_plot_server.R tests/testthat/test-cellimage_plot_ui.R tests/testthat/test-cellimage_server.R tests/testthat/test-cellimage_ui.R tests/testthat/test-clinical_outcomes_functions.R tests/testthat/test-clinical_outcomes_heatmap_server.R tests/testthat/test-clinical_outcomes_server.R tests/testthat/test-clinical_outcomes_survival_server.R tests/testthat/test-clinical_outcomes_survival_ui.R tests/testthat/test-clinical_outcomes_ui.R tests/testthat/test-copy_number_functions.R tests/testthat/test-copy_number_response_server.R tests/testthat/test-copy_number_response_ui.R tests/testthat/test-copy_number_server.R tests/testthat/test-copy_number_ui.R tests/testthat/test-data_info_functions.R tests/testthat/test-data_info_server.R tests/testthat/test-data_table_server.R tests/testthat/test-driver_associations_server.R tests/testthat/test-driver_associations_ui.R tests/testthat/test-extracellular_network_functions.R tests/testthat/test-extracellular_network_main_server.R tests/testthat/test-extracellular_network_main_ui.R tests/testthat/test-extracellular_network_server.R tests/testthat/test-extracellular_network_ui.R tests/testthat/test-immune_feature_correlations_server.R tests/testthat/test-immune_feature_correlations_ui.R tests/testthat/test-immune_feature_distributions_server.R tests/testthat/test-immune_features_server.R tests/testthat/test-immune_features_ui.R tests/testthat/test-immune_subtype_classifier_ui.R tests/testthat/test-immunomodulator_distributions_server.R tests/testthat/test-immunomodulator_distributions_ui.R tests/testthat/test-immunomodulators_functions.R tests/testthat/test-immunomodulators_server.R tests/testthat/test-immunomodulators_ui.R tests/testthat/test-io_target_distributions_server.R tests/testthat/test-io_target_functions.R tests/testthat/test-io_targets_ui.R tests/testthat/test-model_selection_functions.R tests/testthat/test-model_selection_server.R tests/testthat/test-model_selection_ui.R tests/testthat/test-til_map_datatable_functions.R tests/testthat/test-til_map_datatable_server.R tests/testthat/test-til_map_datatable_ui.R tests/testthat/test-til_map_distributions_server.R tests/testthat/test-til_map_distributions_ui.R tests/testthat/test-til_map_server.R tests/testthat/test-til_map_ui.R tests/testthat/test-til_maps_functions.R tests/testthat/test-tumor_microenvironment_cell_proportions_server.R tests/testthat/test-tumor_microenvironment_cell_proportions_ui.R tests/testthat/test-tumor_microenvironment_server.R tests/testthat/test-tumor_microenvironment_type_fractions_server.R tests/testthat/test-tumor_microenvironment_type_fractions_ui.R tests/testthat/test-tumor_microenvironment_ui.R ui.R