https://github.com/saezlab/phonemes
PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics
https://github.com/saezlab/phonemes
Last synced: over 1 year ago
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PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics
- Host: GitHub
- URL: https://github.com/saezlab/phonemes
- Owner: saezlab
- License: gpl-3.0
- Created: 2015-08-07T10:20:45.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2024-04-29T13:42:26.000Z (about 2 years ago)
- Last Synced: 2025-03-28T05:51:02.570Z (over 1 year ago)
- Language: R
- Homepage: https://saezlab.github.io/PHONEMeS
- Size: 188 MB
- Stars: 7
- Watchers: 7
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# PHONEMeS 
## Overview
`PHONEMeS` (**PHO**sphorylation **NE**tworks for **M**ass **S**pectrometry) is a method to model signalling networks based on untargeted phosphoproteomics mass spectrometry data and kinase/phosphatase-substrate interactions.
It is an extension of the Causal Reasoning tool `CARNIVAL` and focuses on identifying deregulated
signaling pathways by linking deregulated phosphorylation sites towards up-stream kinases. Additionally,
it provides prior knowledge networks of kinase-substrate and protein-protein interactions extracted
from `OmnipathR`.
For more information about this package, please check the following links:
- [PHONEMeS vignette](https://github.com/saezlab/PHONEMeS/blob/master/vignettes/PHONEMeS.Rmd) (currently in development)
- [PHONEMeS tutorial](https://github.com/saezlab/PHONEMeS/blob/master/vignettes/tutorial.md)
## Installation
To install `PHONEMeS` please run:
```
devtools::install_github('saezlab/PHONEMeS')
```
### Prerequisites
`PHONEMeS` requires the interactive version of IBM Cplex or CBC-COIN solver as the network
optimiser. The IBM ILOG Cplex is freely available through Academic Initiative [here](https://www.ibm.com/products/ilog-cplex-optimization-studio). The [CBC](https://projects.coin-or.org/Cbc) solver is open source and freely available
for any user. Alternatively for smaller cases, users can rely on the freely available
[lpSolve R-package](https://cran.r-project.org/web/packages/lpSolve/index.html).
## Prior versions
The code for the original PHONEMeS package (PHONEMeS v1.0.0) as described in Terfve et al. 2015 can be found in the releases.
For a guide how to run a PHONEMeS analysis using PHONEMeS v1.0.0, please refer to the [documentation](https://saezlab.github.io/PHONEMeS).
## Citation
[Terfve et al.](http://www.nature.com/articles/ncomms9033):
> Terfve, C. D. A., Wilkes, E. H., Casado, P., Cutillas, P. R., and Saez-Rodriguez, J. (2015). Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data. *Nature Communications*, 6:8033.