fbar: An Extensible Approach to Flux Balance Analysis (original) (raw)
A toolkit for Flux Balance Analysis and related metabolic modeling techniques. Functions are provided for: parsing models in tabular format, converting parsed metabolic models to input formats for common linear programming solvers, and evaluating and applying gene-protein-reaction mappings. In addition, there are wrappers to parse a model, select a solver, find the metabolic fluxes, and return the results applied to the original model. Compared to other packages in this field, this package puts a much heavier focus on providing reusable components that can be used in the design of new implementation of new techniques, in particular those that involve large parameter sweeps. For a background on the theory, see What is Flux Balance Analysis <doi:10.1038/nbt.1614>.
| Version: | 0.6.0 |
|---|---|
| Depends: | R (≥ 3.3.0) |
| Imports: | assertthat, dplyr, magrittr, Matrix, purrr, rlang, ROI, ROI.plugin.ecos, stringr, tibble, tidyr |
| Suggests: | spelling, jsonlite, curl, knitr, rmarkdown, testthat |
| Published: | 2020-09-02 |
| DOI: | 10.32614/CRAN.package.fbar |
| Author: | Max Conway [aut, cre] |
| Maintainer: | Max Conway <conway.max1 at gmail.com> |
| BugReports: | https://github.com/maxconway/fbar/issues |
| License: | GPL-3 |
| URL: | http://maxconway.github.io/fbar/,https://github.com/maxconway/fbar |
| NeedsCompilation: | no |
| Language: | en-GB |
| Materials: | README NEWS |
| In views: | Omics |
| CRAN checks: | fbar results |
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