Creates an interface to BiGG database, provides a framework for simulation and produces flux graphs


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Documentation for package ‘BiGGR’ version 1.5

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addReact2StoM adds a user defined reaction to stoichiometric matrix
attachMetAbbre Attaches abbreviation prefix "M_" for the metabolite identifiers
attachReactAbbre Attaches abbreviation prefix "R_" for the reaction identifiers
createBiggModel createBiggModel
E.coli_iAF1260 Ecoli dataset with ORFs and thermodynamic information
E.coli_iJR904 Ecoli genome-scale model
getAdjMfromStoM getAdjMfromStoM
getEdgeWidths getEdgeWidths
getFluxGraph Gets graphical representation of a flux distribution
getRates Get Optimized Rates
getSMfromModel Get stochiometric matrix from the model file
getStoichiometricMatrix Get entire stoichiometric matrix from the metabolic reconstruction for a specific organism exported in SBML format
Glycolysis Metabolic reconstruction of Glycolysis pathway
gnel Example graphnel object of Glycolysis pathway
H.pylori_ilT341 H.pylori in silico genome-scale characterization of single and double deletion mutants
H.sapiens_Recon_1 Human metabolic reconstruction
M.barkeri_iAF692 Metabolic reconstruction of M.barkeri
model2hyperdraw Draws a hypergraph representation from a model file
possibleExternals possibleExternals
pruneBiggModel pruneBiggModel
rmvReactFromStoM removes a reaction from the stoichiometric matrix
S.aureus_iSB619 Metabolic reconstruction of S.aureus
S.cerevisiae_iND750 Metabolic reconstruction of S.cerevisiae