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emba  

Ensemble Boolean Model Biomarker Analysis
View on CRAN: Click here


Download and install emba package within the R console
Install from CRAN:
install.packages("emba")

Install from Github:
library("remotes")
install_github("cran/emba")

Install by package version:
library("remotes")
install_version("emba", "0.1.8")



Attach the package and use:
library("emba")
Maintained by
John Zobolas
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-10-21
Latest Update: 2023-04-24
Description:
Analysis and visualization of an ensemble of boolean models for biomarker discovery in cancer cell networks. The package allows to easily load the simulation data results of the DrugLogics software pipeline which predicts synergistic drug combinations in cancer cell lines (developed by the DrugLogics research group in NTNU). It has generic functions that can be used to split a boolean model dataset to model groups with regards to the models predictive performance (number of true positive predictions/Matthews correlation coefficient score) or synergy prediction based on a given set of gold standard synergies and find the average activity difference per network node between all model group pairs. Thus, given user-specific thresholds, important nodes (biomarkers) can be accessed in the sense that they make the models predict specific synergies (synergy biomarkers) or have better performance in general (performance biomarkers). Lastly, if the boolean models have a specific equation form and differ only in their link operator, link operator biomarkers can also be found.
How to cite:
John Zobolas (2019). emba: Ensemble Boolean Model Biomarker Analysis. R package version 0.1.8, https://cran.r-project.org/web/packages/emba
Previous versions and publish date:
0.1.1 (2019-10-21 16:30), 0.1.2 (2020-02-06 11:00), 0.1.4 (2020-04-14 21:20), 0.1.5 (2020-07-01 19:40), 0.1.6 (2020-07-08 07:10), 0.1.7 (2020-09-22 12:50), 0.1.8 (2021-01-07 05:00)
Other packages that cited emba R package
View emba citation profile
Other R packages that emba depends, imports, suggests or enhances
Functions, R codes and Examples using the emba R package
Some associated functions: add_numbers_above_the_bars . assign_link_operator_value_to_equation . biomarker_mcc_analysis . biomarker_synergy_analysis . biomarker_tp_analysis . calculate_mcc . calculate_models_mcc . calculate_models_synergies_fn . calculate_models_synergies_fp . calculate_models_synergies_tn . calculate_models_synergies_tp . construct_network . count_models_that_predict_synergies . emba . filter_network . get_alt_drugname . get_avg_activity_diff_based_on_mcc_clustering . get_avg_activity_diff_based_on_specific_synergy_prediction . get_avg_activity_diff_based_on_synergy_set_cmp . get_avg_activity_diff_based_on_tp_predictions . get_avg_activity_diff_mat_based_on_mcc_clustering . get_avg_activity_diff_mat_based_on_specific_synergy_prediction . get_avg_activity_diff_mat_based_on_tp_predictions . get_avg_link_operator_diff_based_on_synergy_set_cmp . get_avg_link_operator_diff_mat_based_on_mcc_clustering . get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction . get_avg_link_operator_diff_mat_based_on_tp_predictions . get_biomarkers . get_biomarkers_per_type . get_edges_from_topology_file . get_fitness_from_models_dir . get_link_operators_from_models_dir . get_model_names . get_model_predictions . get_models_based_on_mcc_class_id . get_neighbors . get_node_colors . get_node_names . get_observed_model_predictions . get_observed_synergies . get_observed_synergies_per_cell_line . get_perf_biomarkers_per_cell_line . get_stable_state_from_models_dir . get_synergy_biomarkers_from_dir . get_synergy_biomarkers_per_cell_line . get_synergy_comparison_sets . get_synergy_scores . get_synergy_subset_stats . get_unobserved_model_predictions . get_vector_diff . get_x_axis_values . is_comb_element_of . make_barplot_on_models_stats . make_barplot_on_synergy_subset_stats . plot_avg_link_operator_diff_graph . plot_avg_link_operator_diff_graphs . plot_avg_state_diff_graph . plot_avg_state_diff_graph_vis . plot_avg_state_diff_graphs . plot_mcc_classes_hist . print_biomarkers_per_predicted_synergy . print_model_and_drug_stats . update_biomarker_files . validate_observed_synergies_data . 
Some associated R codes: analysis.R . biomarkers.R . diff.R . emba.R . general.R . input.R . output.R . plot.R .  Full emba package functions and examples
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