dynafluxr: Retrieve Reaction Rate Dynamics from Metabolite ConcentrationTime Courses
Reaction rate dynamics can be retrieved from metabolite concentration time courses. User has to provide corresponding stoichiometric matrix but not a regulation model (Michaelis-Menten or similar). Instead of solving an ordinary differential equation (ODE) system describing the evolution of concentrations, we use B-splines to catch the concentration and rate dynamics then solve a least square problem on their coefficients with non-negativity (and optionally monotonicity) constraints. Constraints can be also set on initial values of concentration. The package 'dynafluxr' can be used as a library but also as an application with command line interface dynafluxr::cli("-h") or graphical user interface dynafluxr::gui().
| Version: | 1.0.1 |
| Depends: | bspline (≥ 2.5.0),nlsic (≥ 1.1.1) |
| Imports: | optparse,qpdf,arrApply,slam,gmresls (≥ 0.2),shiny,shinyjs,shinyFiles |
| Suggests: | RUnit,knitr |
| Published: | 2025-07-10 |
| DOI: | 10.32614/CRAN.package.dynafluxr |
| Author: | Serguei Sokol [aut, cre] |
| Maintainer: | Serguei Sokol <sokol at insa-toulouse.fr> |
| License: | GPL-2 |
| Copyright: | see fileCOPYRIGHTS |
| NeedsCompilation: | no |
| Materials: | README,NEWS |
| CRAN checks: | dynafluxr results |
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