BiGGR

DOI: 10.18129/B9.bioc.BiGGR  

Constraint based modeling in R using metabolic reconstruction databases

Bioconductor version: Release (3.16)

This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.

Author: Anand K. Gavai, Hannes Hettling

Maintainer: Anand K. Gavai <anand.gavai at bioinformatics.nl>, Hannes Hettling <hannes.hettling at naturalis.nl>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiGGR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BiGGR")

 

PDF	R Script	BiGGR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GraphAndNetwork, Metabolomics, Network, Pathway, Software, Systems Biology, Visualization
Version	1.34.0
In Bioconductor since	BioC 2.13 (R-3.0) (9.5 years)
License	file LICENSE
Depends	R (>= 2.14.0), rsbml, hyperdraw, LIM, stringr
Imports	hypergraph, limSolve
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URL	http://www.bioconductor.org/
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BiGGR_1.34.0.tar.gz
Windows Binary	BiGGR_1.34.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/BiGGR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiGGR
Bioc Package Browser	https://code.bioconductor.org/browse/BiGGR/
Package Short Url	https://bioconductor.org/packages/BiGGR/
Package Downloads Report	Download Stats