Constraint based modeling in R using metabolic reconstruction databases.


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Documentation for package ‘BiGGR’ version 1.2.0

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BiGGR-package Creates an interface to the BiGG database, provides a framework for simulation and produces flux graphs
BiGGR Creates an interface to the BiGG database, provides a framework for simulation and produces flux graphs
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
E.coli_iAF1260 Ecoli dataset with ORFs and thermodynamic information
E.coli_iJR904 Ecoli genome-scale model
E.coli_textbook Ecoli dataset from the BiGG database
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
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
lying.tunell.data Dataset of in vivo cerebral metabolite uptake and release rates in healthy humans (old subjects)
M.barkeri_iAF692 Metabolic reconstruction of M.barkeri from the BiGG database
M.tuberculosis_iNJ661 Metabolic reconstruction of M.tuberculosis from the BiGG database
P.putida_iJN746 Metabolic reconstruction of P.putida 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
sampleFluxEnsemble Sample a posterior ensemble of feasible flux configurations within the precision limits of given fluxes.
sbml2hyperdraw Returns a graph representation of an SBML model