Package: emba
Type: Package
Title: Ensemble Boolean Model Biomarker Analysis
Version: 0.1.6
Authors@R: person("John", "Zobolas", role = c("aut", "cph", "cre"),
email = "bblodfon@gmail.com", comment = c(ORCID = "0000-0002-3609-8674"))
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.
License: MIT + file LICENSE
URL: https://bblodfon.github.io/emba/,
https://github.com/bblodfon/emba,
https://github.com/druglogics/
BugReports: https://github.com/bblodfon/emba/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
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, dplyr, tidyr, tidyselect, stringr, tibble
Suggests: testthat, knitr, rmarkdown, xfun
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-07-08 00:54:00 UTC; john
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-08 05:10:02 UTC