dynafluxr: Retrieve Reaction Rate Dynamics from Metabolite Concentration
Time 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 file COPYRIGHTS |
| NeedsCompilation: |
no |
| Materials: |
README, NEWS |
| CRAN checks: |
dynafluxr results |
Documentation:
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