emba

Spec sheet

Purpose

emba is an R package for analyzing and visualizing biomarkers in ensembles of Boolean models for cancer cell networks.Read 5 Oct 2026 · bblodfon.github.io

Intended users

The package is intended for analysis of Boolean model ensembles, including research into drug synergy and biomarkers in cancer cell networks.Read 5 Oct 2026 · bblodfon.github.io

Support

The project directs users to GitHub Issues to report bugs.Read 5 Oct 2026 · bblodfon.github.io

License

The project page identifies the license as MIT.Read 5 Oct 2026 · bblodfon.github.io

Biomarker discovery

It groups models by predictive performance or synergy prediction and compares average network node activity across model groups to identify biomarkers.Read 5 Oct 2026 · bblodfon.github.io

Biomarker types

The package supports synergy biomarkers, performance biomarkers, and link operator biomarkers for qualifying Boolean models.Read 5 Oct 2026 · bblodfon.github.io

DrugLogics data

The package loads simulation results from DrugLogics, a pipeline used to predict synergistic drug combinations in cancer cell lines.Read 5 Oct 2026 · bblodfon.github.io

Input requirement

Gold-standard drug combinations must be a subset of the combinations tested in the model predictions.Read 5 Oct 2026 · bblodfon.github.io

Inputs

The documented analysis uses model predictions, model stable states, observed gold-standard synergies, and optionally model link operators.Read 5 Oct 2026 · bblodfon.github.io

Install

The project page lists installation from CRAN and a development version installable from GitHub with remotes.Read 5 Oct 2026 · bblodfon.github.io

Performance metrics

Models can be grouped by true positive prediction counts or Matthews correlation coefficient scores.Read 5 Oct 2026 · bblodfon.github.io

Visualization

The guide demonstrates plotting average activity differences and link operator differences on a network graph.Read 5 Oct 2026 · bblodfon.github.io

Where Specifiction places it

• Static Analysis Tools#28 of 386.6