emba: Ensemble Boolean Model Biomarker Analysis

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.

Version: 0.1.8
Depends: R (≥ 2.10)
Imports: graphics, grDevices, utils, purrr, rje (≥ 1.10), igraph (≥ 1.2.4), visNetwork (≥ 2.0.9), Ckmeans.1d.dp (≥ 4.2.2), usefun (≥ 0.4.3), readr (≥ 1.3.0), dplyr (≥ 1.0.0), tidyr (≥ 1.1.0), tidyselect (≥ 1.0.0), stringr (≥ 1.4.0), tibble (≥ 3.0.0)
Suggests: testthat, knitr, rmarkdown, xfun
Published: 2021-01-07
Author: John Zobolas ORCID iD [aut, cph, cre]
Maintainer: John Zobolas <bblodfon at gmail.com>
BugReports: https://github.com/bblodfon/emba/issues
License: MIT + file LICENSE
URL: https://bblodfon.github.io/emba/, https://github.com/bblodfon/emba, https://github.com/druglogics/
NeedsCompilation: no
Materials: README NEWS
CRAN checks: emba results


Reference manual: emba.pdf
Vignettes: emba


Package source: emba_0.1.8.tar.gz
Windows binaries: r-devel: emba_0.1.8.zip, r-release: emba_0.1.8.zip, r-oldrel: emba_0.1.8.zip
macOS binaries: r-release (arm64): emba_0.1.8.tgz, r-release (x86_64): emba_0.1.8.tgz, r-oldrel: emba_0.1.8.tgz
Old sources: emba archive


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