Other packages > Find by keyword >

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:
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. Accessed 25 Jun. 2026.
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

edeaR  
Exploratory and Descriptive Event-Based Data Analysis
Exploratory and descriptive analysis of event based data. Provides methods for describing and select ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
sitmo  
Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files
Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel enviro ...
Download / Learn more Package Citations See dependency  
airGRiwrm  
'airGR' Integrated Water Resource Management
Semi-distributed Precipitation-Runoff Modelling based on 'airGR' package models integrating human i ...
Download / Learn more Package Citations See dependency  
foster  
Forest Structure Extrapolation with R
Set of tools to streamline the modeling of the relationship betweensatellite imagery time series or ...
Download / Learn more Package Citations See dependency  

27,535

R Packages

236,180

Dependencies

73,223

Author Associations

27,536

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA