PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics
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README.md

README.md

PHONEMeS

PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is a method to model signalling networks based on untargeted phosphoproteomics mass spectrometry data and kinase/phosphatase-substrate interactions. Please see Terfve et al. for an explanation of the methodolgy and as an example for how to run a PHONEMeS analysis.

This repository contains the R package and accompanying scripts that implement the method.

License

Distributed under the GNU GPLv2 License. See accompanying file LICENSE.txt or copy at https://www.gnu.org/licenses/gpl-2.0.html.

Installation

For installation, download the tar file of the package and type in R:

install.packages("PHONEMeS_0.2.7.tar.gz", repos=NULL)

Usage

For a guide how to run a PHONEMeS analysis, please refer to the documentation.

References

Terfve et al.:

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.

Wilkes et al. (description of parts of the data)

Wilkes, E. H., Terfve, C., Gribben, J. G., Saez-Rodriguez, J., and Cutillas, P. R. (2015). Empirical inference of circuitry and plasticity in a kinase signaling network. Proceedings of the National Academy of Sciences of the United States of America, 112(25):7719–24.