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emba\n\n\u003c!-- badges: start --\u003e\n[![R build status](https://github.com/bblodfon/emba/workflows/R-CMD-check/badge.svg)](https://github.com/bblodfon/emba/actions)\n[![codecov](https://codecov.io/gh/bblodfon/emba/branch/master/graph/badge.svg)](https://codecov.io/gh/bblodfon/emba)\n[![Downloads](https://cranlogs.r-pkg.org/badges/emba)](https://cran.r-project.org/package=emba)\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.02583/status.svg)](https://doi.org/10.21105/joss.02583)\n\u003c!-- badges: end --\u003e\n\nAnalysis and visualization of an ensemble of boolean models for biomarker discovery in cancer cell networks.\n\nThe package allows to easily load the simulation data results of the [DrugLogics](https://github.com/druglogics) software pipeline that is used to predict synergistic drug combinations in cancer cell lines.\nIt 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.\nThus, 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*).\n\nLastly, if the boolean models have a [specific equation form](https://druglogics.github.io/druglogics-doc/gitsbe-description.html#default-equation) and differ only in their link operator, *link operator* biomarkers can also be found.\n\n## Install\n\nDownload the latest [CRAN archived version](https://cran.r-project.org/src/contrib/Archive/emba/).\n\nDevelopment version:\n```\nremotes::install_github(\"bblodfon/emba\")\n```\n\n## Usage\n\nCheck the [Get Started guide](https://bblodfon.github.io/emba/articles/emba.html).\n\nFor an earlier example usage of this package (version `0.1.1`), see this [analysis](https://druglogics.github.io/gitsbe-model-analysis/atopo/cell-lines-2500/) performed on multiple boolean model datasets.\n\n## Cite\n\n- Formatted citation:\n\nZobolas et al., (2020). emba: R package for analysis and visualization of biomarkers in boolean model ensembles. Journal of Open Source Software, 5(53), 2583, https://doi.org/10.21105/joss.02583\n\n- BibTeX citation:\n```\n@article{Zobolas2020,\n  doi = {10.21105/joss.02583},\n  url = {https://doi.org/10.21105/joss.02583},\n  year = {2020},\n  publisher = {The Open Journal},\n  volume = {5},\n  number = {53},\n  pages = {2583},\n  author = {John Zobolas and Martin Kuiper and Åsmund Flobak},\n  title = {emba: R package for analysis and visualization of biomarkers in boolean model ensembles},\n  journal = {Journal of Open Source Software}\n}\n```\n\n## Code of Conduct\n\nPlease note that the emba project is released with a [Contributor Code of Conduct](https://bblodfon.github.io/emba/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbblodfon%2Femba","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbblodfon%2Femba","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbblodfon%2Femba/lists"}