Files in emba
Ensemble Boolean Model Biomarker Analysis
MD5
LICENSE
NEWS.md
NAMESPACE
DESCRIPTION
README.md
tests/testthat.R
tests/testthat/test-diff.R
tests/testthat/test-general.R
tests/testthat/test-output.R
tests/testthat/test-plot.R
tests/testthat/test-biomarkers.R
tests/testthat/test-input.R
tests/testthat/test-analysis.R
R/plot.R
R/input.R
R/diff.R
R/output.R
R/biomarkers.R
R/analysis.R
R/general.R
R/sysdata.rda
R/emba.R
man/get_observed_synergies.Rd
man/get_node_names.Rd
man/get_synergy_comparison_sets.Rd
man/get_link_operators_from_models_dir.Rd
man/plot_avg_state_diff_graph.Rd
man/get_avg_link_operator_diff_mat_based_on_mcc_clustering.Rd
man/plot_avg_state_diff_graphs.Rd
man/count_models_that_predict_synergies.Rd
man/get_alt_drugname.Rd
man/construct_network.Rd
man/get_avg_activity_diff_based_on_tp_predictions.Rd
man/get_x_axis_values.Rd
man/get_perf_biomarkers_per_cell_line.Rd
man/make_barplot_on_synergy_subset_stats.Rd
man/get_biomarkers_per_type.Rd
man/get_synergy_biomarkers_per_cell_line.Rd
man/get_avg_activity_diff_based_on_synergy_set_cmp.Rd
man/get_models_based_on_mcc_class_id.Rd
man/biomarker_mcc_analysis.Rd
man/get_model_predictions.Rd
man/validate_observed_synergies_data.Rd
man/get_observed_synergies_per_cell_line.Rd
man/get_avg_activity_diff_mat_based_on_mcc_clustering.Rd
man/get_model_names.Rd
man/plot_avg_link_operator_diff_graph.Rd
man/plot_avg_state_diff_graph_vis.Rd
man/get_synergy_scores.Rd
man/emba.Rd
man/calculate_models_mcc.Rd
man/biomarker_synergy_analysis.Rd
man/plot_avg_link_operator_diff_graphs.Rd
man/plot_mcc_classes_hist.Rd
man/calculate_models_synergies_tn.Rd
man/get_avg_link_operator_diff_mat_based_on_tp_predictions.Rd
man/get_unobserved_model_predictions.Rd
man/get_neighbors.Rd
man/calculate_models_synergies_fp.Rd
man/add_numbers_above_the_bars.Rd
man/get_vector_diff.Rd
man/get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction.Rd
man/biomarker_tp_analysis.Rd
man/print_model_and_drug_stats.Rd
man/get_avg_activity_diff_based_on_mcc_clustering.Rd
man/get_node_colors.Rd
man/get_synergy_subset_stats.Rd
man/get_avg_activity_diff_mat_based_on_specific_synergy_prediction.Rd
man/print_biomarkers_per_predicted_synergy.Rd
man/get_avg_link_operator_diff_based_on_synergy_set_cmp.Rd
man/get_avg_activity_diff_mat_based_on_tp_predictions.Rd
man/calculate_models_synergies_tp.Rd
man/calculate_models_synergies_fn.Rd
man/update_biomarker_files.Rd
man/get_observed_model_predictions.Rd
man/get_edges_from_topology_file.Rd
man/calculate_mcc.Rd
man/make_barplot_on_models_stats.Rd
man/get_fitness_from_models_dir.Rd
man/filter_network.Rd
man/get_synergy_biomarkers_from_dir.Rd
man/get_biomarkers.Rd
man/assign_link_operator_value_to_equation.Rd
man/get_stable_state_from_models_dir.Rd
man/is_comb_element_of.Rd
man/get_avg_activity_diff_based_on_specific_synergy_prediction.Rd
inst/extdata/modelwise_synergies
inst/extdata/models_equations
inst/extdata/ensemblewise_synergies
inst/extdata/models_stable_state
inst/extdata/model_predictions
inst/extdata/example.sif
inst/extdata/observed_synergies
inst/extdata/models/test3.gitsbe
inst/extdata/models/test.gitsbe
inst/extdata/models/test2.gitsbe
inst/extdata/models/test4.gitsbe
inst/extdata/biomarkers/A-B_biomarkers_active
inst/extdata/biomarkers/A-B_biomarkers_inhibited
inst/extdata/AGS/bio/biomarkers_active
inst/extdata/AGS/bio/biomarkers_per_synergy
inst/extdata/AGS/bio/biomarkers_inhibited
inst/doc/emba.html
inst/doc/emba.Rmd
inst/doc/emba.R
build/vignette.rds
build/partial.rdb
vignettes/emba.Rmd
