Files in biomedbigdata/SPONGE

Sparse Partial Correlations On Gene Expression

R/biomarker_plots.R R/data.R R/fn_benchmark.R R/fn_check_and_convert_expr_data.R R/fn_elastic_net.R R/fn_gene_miRNA_F_test.R R/fn_gene_miRNA_regression_models.R R/fn_network_centralities.R R/fn_plot_simulation_results.R R/fn_plots.R R/fn_significance.R R/fn_simulation.R R/fn_sponge.R R/fn_spongeffects_utility.R R/fn_subsampling.R README.md man/Random_spongEffects.Rd man/build_classifier_central_genes.Rd man/calibrate_model.Rd man/ceRNA_interactions.Rd man/check_and_convert_expression_data.Rd man/define_modules.Rd man/enrichment_modules.Rd man/ensembl.df.Rd man/filter_ceRNA_network.Rd man/fn_OE_module.Rd man/fn_RF_classifier.Rd man/fn_combined_centrality.Rd man/fn_discretize_spongeffects.Rd man/fn_elasticnet.Rd man/fn_exact_match_summary.Rd man/fn_filter_network.Rd man/fn_gene_miRNA_F_test.Rd man/fn_get_model_coef.Rd man/fn_get_rss.Rd man/fn_get_semi_random_OE.Rd man/fn_get_shared_miRNAs.Rd man/fn_weighted_degree.Rd man/gene_expr.Rd man/genes_pairwise_combinations.Rd man/get_central_modules.Rd man/mir_expr.Rd man/mir_interactions.Rd man/mircode_ensg.Rd man/mircode_symbol.Rd man/plot_accuracy_sensitivity_specificity.Rd man/plot_confusion_matrices.Rd man/plot_density_scores.Rd man/plot_heatmaps.Rd man/plot_involved_miRNAs_to_modules.Rd man/plot_miRNAs_per_gene.Rd man/plot_target_gene_expressions.Rd man/plot_top_modules.Rd man/precomputed_cov_matrices.Rd man/precomputed_null_model.Rd man/prepare_metabric_for_spongEffects.Rd man/prepare_tcga_for_spongEffects.Rd man/sample_zero_mscor_cov.Rd man/sample_zero_mscor_data.Rd man/sponge.Rd man/sponge_build_null_model.Rd man/sponge_compute_p_values.Rd man/sponge_edge_centralities.Rd man/sponge_gene_miRNA_interaction_filter.Rd man/sponge_network.Rd man/sponge_node_centralities.Rd man/sponge_plot_network.Rd man/sponge_plot_network_centralities.Rd man/sponge_plot_simulation_results.Rd man/sponge_run_benchmark.Rd man/sponge_subsampling.Rd man/targetscan_ensg.Rd man/targetscan_symbol.Rd man/test_cancer_gene_expr.Rd man/test_cancer_metadata.Rd man/test_cancer_mir_expr.Rd man/train_cancer_gene_expr.Rd man/train_cancer_metadata.Rd man/train_cancer_mir_expr.Rd man/train_ceRNA_interactions.Rd man/train_network_centralities.Rd spongEffects_logo/SpongEffekt.pdf tests/testthat.R tests/testthat/test_cor_df_cut.R tests/testthat/test_elastic_net.R tests/testthat/test_network_analysis.R tests/testthat/test_regression_filter.R tests/testthat/test_significance.R tests/testthat/test_simulation.R tests/testthat/test_sponge.R vignettes/SPONGE.Rmd vignettes/spongEffects.Rmd