BiGGR: Constraint based modeling in R using metabolic reconstruction databases

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.

AuthorAnand K. Gavai, Hannes Hettling
Date of publicationNone
MaintainerAnand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling <hannes.hettling@naturalis.nl>
Licensefile LICENSE
Version1.10.0
http://www.bioconductor.org/

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...

Functions

BiGGR Man page
BiGGR-package Man page
buildSBMLFromBiGG Man page
buildSBMLFromGenes Man page
buildSBMLFromPathways Man page
buildSBMLFromReactionIDs Man page
.buildSubModel Man page
createLIMFromBiGG Man page
createLIMFromSBML Man page
E.coli_iAF1260 Man page
E.coli_iJR904 Man page
E.coli_textbook Man page
extractGeneAssociations Man page
extractPathways Man page
getPathwaysForSBML Man page
getRates Man page
Glycolysis Man page
gprMapping Man page
gprMappingAvg Man page
H.pylori_ilT341 Man page
H.sapiens_Recon_1 Man page
lying.tunell.data Man page
M.barkeri_iAF692 Man page
M.tuberculosis_iNJ661 Man page
P.putida_iJN746 Man page
Recon2 Man page
rmvSpliceVariant Man page
sampleFluxEnsemble Man page
S.aureus_iSB619 Man page
sbml2hyperdraw Man page
S.cerevisiae_iND750 Man page

Files

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

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