Package: fbar 0.6.0
fbar: An Extensible Approach to Flux Balance Analysis
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>.
Authors:
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fbar.pdf |fbar.html✨
fbar/json (API)
NEWS
| # Install 'fbar' in R: |
| install.packages('fbar', repos = c('https://maxconway.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/maxconway/fbar/issues
- ecoli_core - A small E. coli model, created from a number of sources.
- iJO1366 - A full size E. coli model.
- nutrient_types - A subset of exchange reactions annotated to indicate typical availability
Last updated 4 years agofrom:6619facb92. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 11 2024 |
| R-4.5-win | OK | Nov 11 2024 |
| R-4.5-linux | OK | Nov 11 2024 |
| R-4.4-win | OK | Nov 11 2024 |
| R-4.4-mac | OK | Nov 11 2024 |
| R-4.3-win | OK | Nov 11 2024 |
| R-4.3-mac | OK | Nov 11 2024 |
Exports:decompose_metabolitesexpanded_to_glpkexpanded_to_gurobiexpanded_to_reactiontblexpanded_to_ROIfind_flux_variability_dffind_fluxes_dfgene_associategene_evalget_BiGGreactiontbl_to_expandedreactiontbl_to_gurobirecompose_metabolites
Dependencies:assertthatbackportscheckmateclicpp11dplyrECOSolveRfansigenericsgluelatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6registryrlangROIROI.plugin.ecosslamstringistringrtibbletidyrtidyselectutf8vctrswithr
Introduction
Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 11 2024.Last update: 2020-09-02
Started: 2015-07-19
Multi-Objective Optimization case study
Rendered fromMulti-Objective_Optimization_case_study.Rmdusingknitr::rmarkdownon Nov 11 2024.Last update: 2018-11-18
Started: 2017-01-13
Tutorial
Rendered fromTutorial.Rmdusingknitr::rmarkdownon Nov 11 2024.Last update: 2017-09-23
Started: 2017-01-12
