https://github.com/bblodfon/emba
Ensemble Model Biomarker Analysis R package
https://github.com/bblodfon/emba
biomarkers ensemble-models r r-package
Last synced: 10 months ago
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Ensemble Model Biomarker Analysis R package
- Host: GitHub
- URL: https://github.com/bblodfon/emba
- Owner: bblodfon
- License: other
- Created: 2019-06-03T09:06:29.000Z (almost 7 years ago)
- Default Branch: main
- Last Pushed: 2023-04-26T13:45:46.000Z (about 3 years ago)
- Last Synced: 2025-07-08T02:18:17.319Z (11 months ago)
- Topics: biomarkers, ensemble-models, r, r-package
- Language: R
- Homepage: https://bblodfon.github.io/emba/
- Size: 13.5 MB
- Stars: 0
- Watchers: 1
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# emba
[](https://github.com/bblodfon/emba/actions)
[](https://codecov.io/gh/bblodfon/emba)
[](https://cran.r-project.org/package=emba)
[](https://doi.org/10.21105/joss.02583)
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](https://github.com/druglogics) software pipeline that is used to predict synergistic drug combinations in cancer cell lines.
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](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.
## Install
Download the latest [CRAN archived version](https://cran.r-project.org/src/contrib/Archive/emba/).
Development version:
```
remotes::install_github("bblodfon/emba")
```
## Usage
Check the [Get Started guide](https://bblodfon.github.io/emba/articles/emba.html).
For 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.
## Cite
- Formatted citation:
Zobolas 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
- BibTeX citation:
```
@article{Zobolas2020,
doi = {10.21105/joss.02583},
url = {https://doi.org/10.21105/joss.02583},
year = {2020},
publisher = {The Open Journal},
volume = {5},
number = {53},
pages = {2583},
author = {John Zobolas and Martin Kuiper and Åsmund Flobak},
title = {emba: R package for analysis and visualization of biomarkers in boolean model ensembles},
journal = {Journal of Open Source Software}
}
```
## Code of Conduct
Please 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.