metaboGSE: Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data

metaboGSE depends on the sybil package and was evaluated with GLPK and COIN-OR Clp solvers via the glpkAPI and clpAPI packages, respectively, available in CRAN. The solvers and their R interface API package are not automatically installed along with metaboGSE. The simplex method from GLPK and inibarrier method from Clp were investigated and yielded identical results. glpkAPI simplex was observed to be somehow faster. Other solvers and methods implemented for sybil should also work, however have not been tested. Eventually it should be mentioned that metaboGSE is very demanding for the solvers and may reveal sporadic computational instability, possibly due to the solver compilation and execution environment.