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 pageGLMNET packagecall_made
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 pagemorecall_made).
external pageLicensecall_made (RTF, 2 KB)
Download and Installation
Please refer to external pageREADME for MATLABcall_made and external pageREADME for Rcall_made.
Acknowledgements
This work has been supported by the ETH Zurich Research Grant.