BiGGR: Constraint based modeling in R using metabolic reconstruction databases

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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
Date of publication
None
Maintainer
Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling <hannes.hettling@naturalis.nl>
License
file LICENSE
Version
1.10.0
URLs

View on Bioconductor

Man pages

BiGGR-internal
Internal BiGGR functions and objects
BiGGR-package
Creates an interface to the BiGG database, provides a...
buildSBMLFromBiGG
Build an SBML model from a given reactions file obtained from...
buildSBMLFromGenes
Build an SBML model for specific genes in a given database
buildSBMLFromPathways
Build an SBML model for specific pathway(s) in a given...
buildSBMLFromReactionIDs
Build an SBML model for specific reactions in a given...
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...
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...
H.sapiens_Recon1
Reconstruction of human metabolism from the BiGG database
lying.tunell.data
Dataset of in vivo cerebral metabolite uptake and release...
M.barkeri_iAF692
Metabolic reconstruction of M.barkeri from the BiGG database
M.tuberculosis_iNJ661
Metabolic reconstruction of M.tuberculosis from the BiGG...
P.putida_iJN746
Metabolic reconstruction of P.putida from the BiGG database
Recon2
Human metabolic reconstruction Recon2
rmvSpliceVariant
Remove splicing variants from the database.
sampleFluxEnsemble
Sample a posterior ensemble of feasible flux configurations...
S.aureus_iSB619
Metabolic reconstruction of S.aureus from the BiGG database
sbml2hyperdraw
Returns a graph representation of an SBML model
S.cerevisiae_iND750
Metabolic reconstruction of S.cerevisiae from the BiGG...

Files in this package

BiGGR/.BBSoptions
BiGGR/BiGGR.Rproj
BiGGR/DESCRIPTION
BiGGR/LICENSE
BiGGR/NAMESPACE
BiGGR/R
BiGGR/R/BiGGR-internal.R
BiGGR/R/buildSBMLFromBiGG.R
BiGGR/R/buildSBMLFromGenes.R
BiGGR/R/buildSBMLFromPathways.R
BiGGR/R/buildSBMLFromReactionIDs.R
BiGGR/R/createLIMFromBiGG.R
BiGGR/R/createLIMFromSBML.R
BiGGR/R/extractGeneAssociations.R
BiGGR/R/extractPathways.R
BiGGR/R/getPathwaysForSBML.R
BiGGR/R/getRates.R
BiGGR/R/gprMapping.R
BiGGR/R/gprMappingAvg.R
BiGGR/R/rmvSpliceVariant.R
BiGGR/R/sampleFluxEnsemble.R
BiGGR/R/sbml2hyperdraw.R
BiGGR/build
BiGGR/build/vignette.rds
BiGGR/data
BiGGR/data/E.coli_iAF1260.rda
BiGGR/data/E.coli_iJR904.rda
BiGGR/data/E.coli_textbook.rda
BiGGR/data/Glycolysis.rda
BiGGR/data/H.pylori_ilT341.rda
BiGGR/data/H.sapiens_Recon_1.rda
BiGGR/data/M.barkeri_iAF692.rda
BiGGR/data/M.tuberculosis_iNJ661.rda
BiGGR/data/P.putida_iJN746.rda
BiGGR/data/Recon2.rda
BiGGR/data/S.aureus_iSB619.rda
BiGGR/data/S.cerevisiae_iND750.rda
BiGGR/data/datalist
BiGGR/data/lying.tunell.data.rda
BiGGR/inst
BiGGR/inst/CITATION
BiGGR/inst/COPYRIGHTS
BiGGR/inst/NEWS.Rd
BiGGR/inst/doc
BiGGR/inst/doc/BiGGR.R
BiGGR/inst/doc/BiGGR.Rnw
BiGGR/inst/doc/BiGGR.pdf
BiGGR/inst/extdata
BiGGR/inst/extdata/Gene_Symbol_Entrez_Foldchanges.csv
BiGGR/inst/extdata/Glycolysis.LIM
BiGGR/inst/extdata/Glycolysis_TCA.LIM
BiGGR/inst/extdata/Glycolysis_TCA_recon1_reactionIDs.txt
BiGGR/inst/extdata/Glycolysis_TCA_recon2_reactionIDs.txt
BiGGR/inst/extdata/Reactions.txt
BiGGR/inst/extdata/brainmodel_reactions.txt
BiGGR/man
BiGGR/man/BiGGR-internal.Rd
BiGGR/man/BiGGR-package.Rd
BiGGR/man/E.coli_iAF1260.Rd
BiGGR/man/E.coli_iJR904.Rd
BiGGR/man/E.coli_textbook.Rd
BiGGR/man/Glycolysis.Rd
BiGGR/man/H.pylori_ilT341.Rd
BiGGR/man/H.sapiens_Recon1.Rd
BiGGR/man/M.barkeri_iAF692.Rd
BiGGR/man/M.tuberculosis_iNJ661.Rd
BiGGR/man/P.putida_iJN746.Rd
BiGGR/man/Recon2.Rd
BiGGR/man/S.aureus_iSB619.Rd
BiGGR/man/S.cerevisiae_iND750.Rd
BiGGR/man/buildSBMLFromBiGG.Rd
BiGGR/man/buildSBMLFromGenes.Rd
BiGGR/man/buildSBMLFromPathways.Rd
BiGGR/man/buildSBMLFromReactionIDs.Rd
BiGGR/man/createLIMFromBiGG.Rd
BiGGR/man/createLIMFromSBML.Rd
BiGGR/man/extractGeneAssociations.Rd
BiGGR/man/extractPathways.Rd
BiGGR/man/getPathwaysForSBML.Rd
BiGGR/man/getRates.Rd
BiGGR/man/gprMapping.Rd
BiGGR/man/gprMappingAvg.Rd
BiGGR/man/lying.tunell.data.Rd
BiGGR/man/rmvSpliceVariant.Rd
BiGGR/man/sampleFluxEnsemble.Rd
BiGGR/man/sbml2hyperdraw.Rd
BiGGR/vignettes
BiGGR/vignettes/BiGGR.Rnw
BiGGR/vignettes/BiGGR.bib