emba
emba: R package for analysis and visualization of biomarkers in boolean model ensembles - Published in JOSS (2020)
Science Score: 93.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 9 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org -
○Committers with academic emails
-
○Institutional organization owner
-
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Scientific Fields
Repository
Ensemble Model Biomarker Analysis R package
Basic Info
- Host: GitHub
- Owner: bblodfon
- License: other
- Language: R
- Default Branch: main
- Homepage: https://bblodfon.github.io/emba/
- Size: 13.5 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 3
- Open Issues: 0
- Releases: 9
Topics
Metadata Files
README.md
emba
<!-- badges: end -->
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 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 and differ only in their link operator, link operator biomarkers can also be found.
Install
Download the latest CRAN archived version.
Development version:
remotes::install_github("bblodfon/emba")
Usage
Check the Get Started guide.
For an earlier example usage of this package (version 0.1.1), see this analysis 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. By contributing to this project, you agree to abide by its terms.
Owner
- Name: John Zobolas
- Login: bblodfon
- Kind: user
- Repositories: 13
- Profile: https://github.com/bblodfon
JOSS Publication
emba: R package for analysis and visualization of biomarkers in boolean model ensembles
Authors
Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, The Cancer Clinic, St. Olav’s Hospital, Trondheim, Norway
Editor
Mikkel Meyer Andersen
Tags
boolean networks logical modeling biomarkers mechanistic models drug synergies anti-cancer drug combinations druglogicsGitHub Events
Total
Last Year
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| john | b****n@g****m | 243 |
| Arfon Smith | a****n | 1 |
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 2
- Total pull requests: 1
- Average time to close issues: 2 days
- Average time to close pull requests: about 3 hours
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 2.5
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- edifice1989 (1)
- mikldk (1)
Pull Request Authors
- arfon (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 271 last-month
- Total docker downloads: 21,613
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
cran.r-project.org: emba
Ensemble Boolean Model Biomarker Analysis
- Homepage: https://bblodfon.github.io/emba/
- Documentation: http://cran.r-project.org/web/packages/emba/emba.pdf
- License: MIT + file LICENSE
- Status: removed
-
Latest release: 0.1.8
published almost 5 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 2.10 depends
- Ckmeans.1d.dp >= 4.2.2 imports
- dplyr >= 1.0.0 imports
- grDevices * imports
- graphics * imports
- igraph >= 1.2.4 imports
- purrr * imports
- readr >= 1.3.0 imports
- rje >= 1.10 imports
- stringr >= 1.4.0 imports
- tibble >= 3.0.0 imports
- tidyr >= 1.1.0 imports
- tidyselect >= 1.0.0 imports
- usefun >= 0.4.3 imports
- utils * imports
- visNetwork >= 2.0.9 imports
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
- xfun * suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite