Package: emba
Type: Package
Title: Ensemble Boolean Model Biomarker Analysis
Version: 0.1.8
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 (>= 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
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-01-06 11:00:44 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: 2021-01-07 04:00:02 UTC
Built: R 4.1.3; ; 2023-04-17 18:30:46 UTC; windows
