Files in mlist/SPONGE
Sparse Partial Correlations On Gene Expression
.Rbuildignore
.gitignore
.idea/workspace.xml
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
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
data/ceRNA_interactions.RData
data/ensembl.df.RData
data/gene_expr.RData
data/mir_expr.RData
data/mir_interactions.RData
data/mircode.RData
data/precomputed_null_model.rda
data/scor_simulation_cov_matrices.RData
data/targetscan.RData
data/test_cancer_gene_expr.RData
data/test_cancer_metadata.RData
data/test_cancer_mir_expr.RData
data/train_cancer_gene_expr.RData
data/train_cancer_metadata.RData
data/train_cancer_mir_expr.RData
data/train_ceRNA_interactions.RData
data/train_genes_miRNA_candidates.RData
data/train_network_centralities.RData
inst/CITATION
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/Endprodukt_Schrift rechts.png
spongEffects_logo/Endprodukt_Schrift unten.png
spongEffects_logo/SpongEffekt.pdf
spongEffects_logo/SpongEffekt_Endprodukt_Logo alleinstehend.png
sponge_logo.svg
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/overview.png
vignettes/spongEffects.Rmd
vignettes/sponge_logo.png
vignettes/sponge_logo.svg
