DynafluxR is a software for dynamic metabolic flux analysis and is available from this repository.
DynafluxR can be used as an R package that you can import directly, for instance in R Markdown notebooks or in your own software.
We showcase DynafluxR usage with step-by-step examples in a R Markdown notebook distributed via this repository. We also distribute an HTML file showing the notebook’s output after execution.
This R code perform all analyses detailed in the following publication:
Estimating flux dynamics from metabolite concentration time courses with dynafluxr.
Sokol S., Dubiley S., Rouan P., Charlier C., Lippens G., Millard P. bioRxiv preprint, 2025, doi: 10.1101/2025.07.22.666125
Details on the calculations can be found in the publication and in the Rmd notebook.
The code is open-source and available under GPLv3 license.
If not yet done, download and install Rstudio.
Some required dependencies are specific to our notebook, not to DynafluxR itself.
RColorBrewer, stringr, and vioplot can be installed
by running the following command in the Rstudio console:
install.packages(c("RColorBrewer", "stringr", "vioplot"))CoRC can be installed
using the following commands:
install.packages("remotes")
library(remotes)
remotes::install_github("jpahle/CoRC")
library(CoRC)
CoRC::getCopasi()Additional information on CoRC installation and usage are available from the CoRC repository (https://github.com/jpahle/CoRC) and the associated publication (Föster et al., Bioinformatics, 2021, doi: 10.1093/bioinformatics/btab033).
To run all analyses detailed in the publication and reproduce Figures 3 and 4:
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download the GitHub repository tarball and unpack it somewhere on your disk
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start RStudio
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open the file
./notebook.Rmd
The notebook will open in Rstudio, in each cell you can read/modify/execute the code as well as read accompanying comments.
If you have any question, please open a new issue to our GitHub issue tracker so we could discuss together.
Serguei Sokol, Svetlana Dubiley, Pauline Rouan, Cyril Charlier, Guy Lippens, Pierre Millard. Estimating flux dynamics from metabolite concentration time courses with dynafluxr. bioRxiv preprint, 2025, doi: 10.1101/2025.07.22.666125.
Sergueï Sokol, Pierre Millard