R: Creates an interface to the BiGG database, provides a...
BiGGR-package
R Documentation
Creates an interface to the BiGG database, provides a framework for simulation and produces flux graphs
Description
This package provides an interface to simulate metabolic reconstruction
from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction
databases. The package aids in performing flux balance analysis (FBA).
Metabolic networks and estimated fluxes can be visualized
using hypergraphs.
Details
Package:
BiGGR
Type:
Package
Version:
0.99.0
Date:
2013-07-10
Depends:
R (>= 2.14.0), rsbml, hyperdraw, LIM
Imports:
hypergraph
License:
GPL (>=2)
URL:
http://www.bioconductor.org/
Copyright:
see inst/COPYRIGHTS for the license of the BiGG database
biocViews:
NetworkAnalysis, Visualization, Metabolomics
LazyLoad:
yes
Packaged:
2013-08-05 12:44:08 UTC; hettling
Built:
R 3.0.0; ; 2013-08-05 12:44:22 UTC; unix
Index:
E.coli_iAF1260 Ecoli dataset with ORFs and thermodynamic information
E.coli_iJR904 Ecoli genome-scale model
Glycolysis Metabolic reconstruction of Glycolysis pathway
H.pylori_ilT341 H.pylori in silico genome-scale characterization of single and double deletion mutants
H.sapiens_Recon_1 Reconstruction of human metabolism from the BiGG database
M.barkeri_iAF692 Metabolic reconstruction of M.barkeri from the BiGG database
Recon2 Human metabolic reconstruction Recon2
S.aureus_iSB619 Metabolic reconstruction of S.aureus from the BiGG database
S.cerevisiae_iND750 Metabolic reconstruction of S.cerevisiae from the BiGG database
buildSBMLFromBiGG Build an SBML model from a given reactions file obtained from the BiGG database
buildSBMLFromGenes Build an SBML model for specific genes in a given database
buildSBMLFromPathways Build an SBML model for specific pathway(s) in a given database
buildSBMLFromReactionIDs Build an SBML model for specific reactions in a given database
createLIMFromBiGG Create a LIM model object from a BiGG database file
createLIMFromSBML Create a LIM model object from an SBML file
extractGeneAssociations Extract informations on genes from a given database
extractPathways Extract all pathways from given database
getPathwaysForSBML Extract all pathways from a database that are relevant for a given SBML model
getRates Get Optimized Rates
sbml2hyperdraw Returns a graph representation of an SBML model
Further information is available in the following vignettes:
BiGGR
BiGGR (source, pdf)
Author(s)
Anand K. Gavai, Hannes Hettling
Maintainer: Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling <j.hettling@vu.nl>
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BiGGR)
Error in library(BiGGR) : there is no package called 'BiGGR'
Execution halted