emba

Free plan Linux

What emba is

emba is a free R package for examining biomarkers in ensembles of Boolean models that represent cancer cell networks. It loads simulation results from DrugLogics, a pipeline for predicting synergistic drug combinations in cancer cell lines. You can group models by predictive performance or synergy prediction, then compare average activity of network nodes between groups to find possible biomarkers. Grouping can use true-positive prediction counts or Matthews correlation coefficient scores. The package covers synergy biomarkers, performance biomarkers, and link operator biomarkers for qualifying Boolean models. Its visualizations can plot average activity differences and link operator differences on a network graph. Documented inputs include model predictions, model stable states, observed gold-standard synergies, and optionally model link operators. Gold-standard combinations must be among those tested in the model predictions. emba runs on Linux, is licensed under MIT, and can be installed from CRAN or as a GitHub development version using remotes. Bug reports are directed to GitHub Issues.

Who it suits

emba suits researchers analyzing Boolean model ensembles, especially work on drug synergy and cancer-network biomarkers. It is intended for Linux users working with DrugLogics simulation outputs.

What it does well

Free R package
Groups models by predictive metrics
Supports three biomarker types
Network graph visualizations
CRAN and GitHub installation options

What to know first

Linux platform only
Gold-standard combinations must be tested
Requires model predictions and stable states

Verdict

emba provides a focused workflow for comparing Boolean model groups and finding network biomarkers. Its required inputs and Linux platform should fit the intended research setup.

Facts from emba's own pages

Biomarker discovery: It groups models by predictive performance or synergy prediction and compares average network node activity across model groups to identify biomarkers. · bblodfon.github.io, 5 Oct 2026
Biomarker types: The package supports synergy biomarkers, performance biomarkers, and link operator biomarkers for qualifying Boolean models. · bblodfon.github.io, 5 Oct 2026
DrugLogics data: The package loads simulation results from DrugLogics, a pipeline used to predict synergistic drug combinations in cancer cell lines. · bblodfon.github.io, 5 Oct 2026
Input requirement: Gold-standard drug combinations must be a subset of the combinations tested in the model predictions. · bblodfon.github.io, 5 Oct 2026
Inputs: The documented analysis uses model predictions, model stable states, observed gold-standard synergies, and optionally model link operators. · bblodfon.github.io, 5 Oct 2026
Install: The project page lists installation from CRAN and a development version installable from GitHub with remotes. · bblodfon.github.io, 5 Oct 2026
Intended users: The package is intended for analysis of Boolean model ensembles, including research into drug synergy and biomarkers in cancer cell networks. · bblodfon.github.io, 5 Oct 2026
License: The project page identifies the license as MIT. · bblodfon.github.io, 5 Oct 2026
Performance metrics: Models can be grouped by true positive prediction counts or Matthews correlation coefficient scores. · bblodfon.github.io, 5 Oct 2026
Purpose: emba is an R package for analyzing and visualizing biomarkers in ensembles of Boolean models for cancer cell networks. · bblodfon.github.io, 5 Oct 2026
Support: The project directs users to GitHub Issues to report bugs. · bblodfon.github.io, 5 Oct 2026
Visualization: The guide demonstrates plotting average activity differences and link operator differences on a network graph. · bblodfon.github.io, 5 Oct 2026

Where emba stands on Freedom251

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