Files in cbg-ethz/pareg

Pathway enrichment using a regularized regression approach

NEWS.md R/basilisk.R R/cluster_execution.R R/data.R R/main.R R/netreg.R R/pareg-package.R R/plotting.R R/term_similarities.R R/utils.R README.md data-raw/pathway_similarities.R inst/scripts/exploratory_analysis/README.md inst/scripts/exploratory_analysis/workflow/scripts/extra_stuff.R inst/scripts/exploratory_analysis/workflow/scripts/load_terms.R inst/scripts/exploratory_analysis/workflow/scripts/provide_data.R inst/scripts/exploratory_analysis/workflow/scripts/run_pareg.R inst/scripts/exploratory_analysis/workflow/scripts/visualize.R inst/scripts/synthetic_benchmark/README.md inst/scripts/synthetic_benchmark/resources/method_definitions/blitzgsea.R inst/scripts/synthetic_benchmark/resources/method_definitions/fgsea.R inst/scripts/synthetic_benchmark/resources/method_definitions/gsea.R inst/scripts/synthetic_benchmark/resources/method_definitions/mgsa.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_ber.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_bernoulli.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_beta.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_beta_lm.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_beta_var.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_clip.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_gau.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_gaussian.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_lasso.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_10.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_100.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_1000.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_10000.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_ber.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_cv.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_cv_bum.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_gau.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_lasso.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_phi_lm.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_network_phi_var.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_ng.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_noterms.R inst/scripts/synthetic_benchmark/resources/method_definitions/pareg_pois.R inst/scripts/synthetic_benchmark/resources/method_definitions/random.R inst/scripts/synthetic_benchmark/resources/method_definitions/single_term_methods.R inst/scripts/synthetic_benchmark/resources/method_definitions/topgo.R inst/scripts/synthetic_benchmark/resources/multi_config_workflow/workflow/scripts/compare_rocauc_vs_loss.R inst/scripts/synthetic_benchmark/workflow/scripts/aggregate_results.R inst/scripts/synthetic_benchmark/workflow/scripts/aggregated_visualization.R inst/scripts/synthetic_benchmark/workflow/scripts/compute_term_similarities.R inst/scripts/synthetic_benchmark/workflow/scripts/create_synthetic_study.R inst/scripts/synthetic_benchmark/workflow/scripts/create_term_database.R inst/scripts/synthetic_benchmark/workflow/scripts/model_setup_code.R inst/scripts/synthetic_benchmark/workflow/scripts/visualize_results.R man/as.data.frame.pareg.Rd man/as_dense_sim.Rd man/as_enrichplot_object.Rd man/cluster_apply.Rd man/compute_term_similarities.Rd man/create_model_df.Rd man/cvedgenet-methods.Rd man/edgenet-methods.Rd man/family-methods.Rd man/generate_similarity_matrix.Rd man/jaccard.Rd man/overlap_coefficient.Rd man/pareg.Rd man/pareg_env.Rd man/pathway_similarities.Rd man/plot.pareg.Rd man/plot_pareg_with_args.Rd man/similarity_sample.Rd man/transform_y.Rd tests/testthat.R tests/testthat/test-netreg.R tests/testthat/test-pareg.R tests/testthat/test-term_similarities.R tests/testthat/test-utils.R vignettes/pareg.Rmd vignettes/pathway_similarities.Rmd