# Constraint based modeling in R using metabolic reconstruction databases

## Documentation for package ‘BiGGR’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
gprMapping | GPR mapping
gprMappingAvg | GPR mapping ignoring AND & OR operators
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
rmvSpliceVariant | Remove splicing variants from the database.
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