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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>.

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

Documentation:

Reference manual: fbar.pdf
Vignettes: Introduction
Multi-Objective Optimization case study
Tutorial

Downloads:

Package source: fbar_0.6.0.tar.gz
Windows binaries: r-devel: fbar_0.6.0.zip, r-release: fbar_0.6.0.zip, r-oldrel: fbar_0.6.0.zip
macOS binaries: r-release (arm64): fbar_0.6.0.tgz, r-oldrel (arm64): fbar_0.6.0.tgz, r-release (x86_64): fbar_0.6.0.tgz, r-oldrel (x86_64): fbar_0.6.0.tgz
Old sources: fbar archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=fbar to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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