SALMON

SALMON (Systems Analysis and Learning for inferring Modifiers of Networks) is a network-based analytical tool for identifying protein targets of compounds from gene transcriptional profiles. SALMON scores proteins according to the enhancement or attenuation of the protein-gene regulatory interactions caused by a compound treatment. The magnitude of the scores indicates the degree of compound-induced alterations in the gene regulatory activity of a protein, while the sign of the scores indicates the direction of the alterations (positive: enhancement, negative: attenuation). In SALMON, the protein targets of a compound are ranked according to the magnitudes of the protein scores.

MATLAB and R versions of SALMON are available. Please refer to SALMON manuscript for more detailed information.

Prerequisites

For MATLAB distribution,

• MATLAB® R2014b or later
• external page GLMNET package

For R distribution,

• R software (>=3.3.2)
• devtools package in R

Last Update

• MATLAB package: version 1.0 (19.07.2017)
• R package: version 1.0 (19.07.2017)

License

Redistribution and use in source and binary forms, with or without modification, are permitted provided agreeing to the Simplified BSD Style License (see external page more).

external page License (RTF, 2 KB)

Download and Installation

Please refer to external page README for MATLAB and external page README for R.

Acknowledgements

This work has been supported by the ETH Zurich Research Grant.