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:

Reference manual:	dynafluxr.pdf
Vignettes:	glyco (source, R code)

Downloads:

Package source:	dynafluxr_1.0.1.tar.gz
Windows binaries:	r-devel: not available, r-release: dynafluxr_1.0.1.zip, r-oldrel: not available
macOS binaries:	r-release (arm64): dynafluxr_1.0.1.tgz, r-oldrel (arm64): dynafluxr_1.0.1.tgz, r-release (x86_64): dynafluxr_1.0.1.tgz, r-oldrel (x86_64): dynafluxr_1.0.1.tgz

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