Files in bblodfon/emba
Ensemble Boolean Model Biomarker Analysis
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/test-coverage.yaml
.gitignore
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/analysis.R
R/biomarkers.R
R/diff.R
R/emba.R
R/general.R
R/input.R
R/output.R
R/plot.R
R/sysdata.rda
README.md
_pkgdown.yml
docs/404.html
docs/CODE_OF_CONDUCT.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/emba.html
docs/articles/emba_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/emba_files/figure-html/mcc-analysis-10-1.png
docs/articles/emba_files/figure-html/mcc-analysis-3-1.png
docs/articles/emba_files/figure-html/mcc-analysis-4-1.png
docs/articles/emba_files/figure-html/mcc-analysis-7-1.png
docs/articles/emba_files/figure-html/synergy-analysis-2-1.png
docs/articles/emba_files/figure-html/synergy-analysis-3-1.png
docs/articles/emba_files/figure-html/synergy-analysis-4-1.png
docs/articles/emba_files/figure-html/synergy-analysis-5-1.png
docs/articles/emba_files/figure-html/tp-analysis-10-1.png
docs/articles/emba_files/figure-html/tp-analysis-3-1.png
docs/articles/emba_files/figure-html/tp-analysis-6-1.png
docs/articles/emba_files/header-attrs-2.1/header-attrs.js
docs/articles/emba_files/header-attrs-2.3/header-attrs.js
docs/articles/emba_files/header-attrs-2.6/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/add_numbers_above_the_bars.html
docs/reference/assign_link_operator_value_to_equation.html
docs/reference/biomarker_mcc_analysis.html
docs/reference/biomarker_synergy_analysis.html
docs/reference/biomarker_tp_analysis.html
docs/reference/calculate_mcc.html
docs/reference/calculate_models_mcc.html
docs/reference/calculate_models_synergies_fn.html
docs/reference/calculate_models_synergies_fp.html
docs/reference/calculate_models_synergies_tn.html
docs/reference/calculate_models_synergies_tp.html
docs/reference/construct_network.html
docs/reference/count_models_that_predict_synergies.html
docs/reference/emba.html
docs/reference/filter_network.html
docs/reference/get_alt_drugname.html
docs/reference/get_avg_activity_diff_based_on_mcc_clustering.html
docs/reference/get_avg_activity_diff_based_on_specific_synergy_prediction.html
docs/reference/get_avg_activity_diff_based_on_synergy_set_cmp.html
docs/reference/get_avg_activity_diff_based_on_tp_predictions.html
docs/reference/get_avg_activity_diff_mat_based_on_mcc_clustering.html
docs/reference/get_avg_activity_diff_mat_based_on_specific_synergy_prediction.html
docs/reference/get_avg_activity_diff_mat_based_on_tp_predictions.html
docs/reference/get_avg_link_operator_diff_based_on_synergy_set_cmp.html
docs/reference/get_avg_link_operator_diff_mat_based_on_mcc_clustering.html
docs/reference/get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction.html
docs/reference/get_avg_link_operator_diff_mat_based_on_tp_predictions.html
docs/reference/get_biomarkers.html
docs/reference/get_biomarkers_per_type.html
docs/reference/get_edges_from_topology_file.html
docs/reference/get_fitness_from_models_dir.html
docs/reference/get_link_operators_from_models_dir.html
docs/reference/get_model_names.html
docs/reference/get_model_predictions.html
docs/reference/get_models_based_on_mcc_class_id.html
docs/reference/get_neighbors.html
docs/reference/get_node_colors.html
docs/reference/get_node_names.html
docs/reference/get_observed_model_predictions.html
docs/reference/get_observed_synergies.html
docs/reference/get_observed_synergies_per_cell_line.html
docs/reference/get_perf_biomarkers_per_cell_line.html
docs/reference/get_stable_state_from_models_dir.html
docs/reference/get_synergy_biomarkers_from_dir.html
docs/reference/get_synergy_biomarkers_per_cell_line.html
docs/reference/get_synergy_comparison_sets.html
docs/reference/get_synergy_scores.html
docs/reference/get_synergy_subset_stats.html
docs/reference/get_unobserved_model_predictions.html
docs/reference/get_vector_diff.html
docs/reference/get_x_axis_values.html
docs/reference/index.html
docs/reference/is_comb_element_of.html
docs/reference/make_barplot_on_models_stats-1.png
docs/reference/make_barplot_on_models_stats.html
docs/reference/make_barplot_on_synergy_subset_stats-1.png
docs/reference/make_barplot_on_synergy_subset_stats.html
docs/reference/plot_avg_link_operator_diff_graph-1.png
docs/reference/plot_avg_link_operator_diff_graph.html
docs/reference/plot_avg_link_operator_diff_graphs.html
docs/reference/plot_avg_state_diff_graph-1.png
docs/reference/plot_avg_state_diff_graph.html
docs/reference/plot_avg_state_diff_graph_vis.html
docs/reference/plot_avg_state_diff_graphs.html
docs/reference/plot_mcc_classes_hist-1.png
docs/reference/plot_mcc_classes_hist.html
docs/reference/print_biomarkers_per_predicted_synergy.html
docs/reference/print_model_and_drug_stats.html
docs/reference/update_biomarker_files.html
docs/reference/validate_observed_synergies_data.html
docs/sitemap.xml
emba.Rproj
inst/extdata/AGS/bio/biomarkers_active
inst/extdata/AGS/bio/biomarkers_inhibited
inst/extdata/AGS/bio/biomarkers_per_synergy
inst/extdata/biomarkers/A-B_biomarkers_active
inst/extdata/biomarkers/A-B_biomarkers_inhibited
inst/extdata/ensemblewise_synergies
inst/extdata/example.sif
inst/extdata/model_predictions
inst/extdata/models/test.gitsbe
inst/extdata/models/test2.gitsbe
inst/extdata/models/test3.gitsbe
inst/extdata/models/test4.gitsbe
inst/extdata/models_equations
inst/extdata/models_stable_state
inst/extdata/modelwise_synergies
inst/extdata/observed_synergies
man/add_numbers_above_the_bars.Rd
man/assign_link_operator_value_to_equation.Rd
man/biomarker_mcc_analysis.Rd
man/biomarker_synergy_analysis.Rd
man/biomarker_tp_analysis.Rd
man/calculate_mcc.Rd
man/calculate_models_mcc.Rd
man/calculate_models_synergies_fn.Rd
man/calculate_models_synergies_fp.Rd
man/calculate_models_synergies_tn.Rd
man/calculate_models_synergies_tp.Rd
man/construct_network.Rd
man/count_models_that_predict_synergies.Rd
man/emba.Rd
man/filter_network.Rd
man/get_alt_drugname.Rd
man/get_avg_activity_diff_based_on_mcc_clustering.Rd
man/get_avg_activity_diff_based_on_specific_synergy_prediction.Rd
man/get_avg_activity_diff_based_on_synergy_set_cmp.Rd
man/get_avg_activity_diff_based_on_tp_predictions.Rd
man/get_avg_activity_diff_mat_based_on_mcc_clustering.Rd
man/get_avg_activity_diff_mat_based_on_specific_synergy_prediction.Rd
man/get_avg_activity_diff_mat_based_on_tp_predictions.Rd
man/get_avg_link_operator_diff_based_on_synergy_set_cmp.Rd
man/get_avg_link_operator_diff_mat_based_on_mcc_clustering.Rd
man/get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction.Rd
man/get_avg_link_operator_diff_mat_based_on_tp_predictions.Rd
man/get_biomarkers.Rd
man/get_biomarkers_per_type.Rd
man/get_edges_from_topology_file.Rd
man/get_fitness_from_models_dir.Rd
man/get_link_operators_from_models_dir.Rd
man/get_model_names.Rd
man/get_model_predictions.Rd
man/get_models_based_on_mcc_class_id.Rd
man/get_neighbors.Rd
man/get_node_colors.Rd
man/get_node_names.Rd
man/get_observed_model_predictions.Rd
man/get_observed_synergies.Rd
man/get_observed_synergies_per_cell_line.Rd
man/get_perf_biomarkers_per_cell_line.Rd
man/get_stable_state_from_models_dir.Rd
man/get_synergy_biomarkers_from_dir.Rd
man/get_synergy_biomarkers_per_cell_line.Rd
man/get_synergy_comparison_sets.Rd
man/get_synergy_scores.Rd
man/get_synergy_subset_stats.Rd
man/get_unobserved_model_predictions.Rd
man/get_vector_diff.Rd
man/get_x_axis_values.Rd
man/is_comb_element_of.Rd
man/make_barplot_on_models_stats.Rd
man/make_barplot_on_synergy_subset_stats.Rd
man/plot_avg_link_operator_diff_graph.Rd
man/plot_avg_link_operator_diff_graphs.Rd
man/plot_avg_state_diff_graph.Rd
man/plot_avg_state_diff_graph_vis.Rd
man/plot_avg_state_diff_graphs.Rd
man/plot_mcc_classes_hist.Rd
man/print_biomarkers_per_predicted_synergy.Rd
man/print_model_and_drug_stats.Rd
man/update_biomarker_files.Rd
man/validate_observed_synergies_data.Rd
paper/paper.bib
paper/paper.md
tests/testthat.R
tests/testthat/test-analysis.R
tests/testthat/test-biomarkers.R
tests/testthat/test-diff.R
tests/testthat/test-general.R
tests/testthat/test-input.R
tests/testthat/test-output.R
tests/testthat/test-plot.R
vignettes/.gitignore
vignettes/data.rds
vignettes/emba.Rmd
