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

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