MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models
The MetPath software package accompanies the manuscript:
[SUBMITTED] "Differential expression analysis utilizing metabolic pathways based on physiological flux states" Gianluca Mattei, Daniel C. Zielinski, Zhuohui Gan, Matteo Ramazzotti, Bernhard O. Palsson
The folders in this package are the following:
core - Functions intended to be called by the user
data files - example files that enable MetPath to be run. can be modified by the user
external - third party code used by the MetPath package. extractGPRs is an internal function from the COBRA toolbox. em_decomp is an external elementary mode calculation package
internal - functions used by MetPath that are not necessarily intended to be directly called by the user
tutorial - example workflow demonstrating use of the MetPath package
Questions and issues can be addressed to Daniel Zielinski at dczielin@ucsd.edu