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BiGGR

Constraint based modeling in R using metabolic reconstruction databases

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("BiGGR")):

Installation

To install this package, start R (version "4.3") 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")
BiGGR PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GraphAndNetwork, Metabolomics, Network, Pathway, Software, Systems Biology, Visualization
Version 1.36.0
In Bioconductor since BioC 2.13 (R-3.0) (10 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_1.36.0.tar.gz
Windows Binary BiGGR_1.36.0.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