BiGGR: Constraint based modeling in R using metabolic reconstruction databases
Version 1.12.0

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
Bioconductor views GraphAndNetwork Metabolomics Network Pathway Systems Biology Visualization
Date of publicationNone
MaintainerAnand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling <hannes.hettling@naturalis.nl>
Licensefile LICENSE
Version1.12.0
URL http://www.bioconductor.org/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BiGGR")

Getting started

Package overview

Popular man pages

E.coli_textbook: Ecoli dataset from the BiGG database
M.barkeri_iAF692: Metabolic reconstruction of M.barkeri from the BiGG database
M.tuberculosis_iNJ661: Metabolic reconstruction of M.tuberculosis from the BiGG...
Recon2: Human metabolic reconstruction Recon2
sampleFluxEnsemble: Sample a posterior ensemble of feasible flux configurations...
sbml2hyperdraw: Returns a graph representation of an SBML model
S.cerevisiae_iND750: Metabolic reconstruction of S.cerevisiae from the BiGG...
See all...

All man pages Function index File listing

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

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

Files

.BBSoptions
BiGGR.Rproj
DESCRIPTION
LICENSE
NAMESPACE
R
R/BiGGR-internal.R
R/buildSBMLFromBiGG.R
R/buildSBMLFromGenes.R
R/buildSBMLFromPathways.R
R/buildSBMLFromReactionIDs.R
R/createLIMFromBiGG.R
R/createLIMFromSBML.R
R/extractGeneAssociations.R
R/extractPathways.R
R/getPathwaysForSBML.R
R/getRates.R
R/gprMapping.R
R/gprMappingAvg.R
R/rmvSpliceVariant.R
R/sampleFluxEnsemble.R
R/sbml2hyperdraw.R
build
build/vignette.rds
data
data/E.coli_iAF1260.rda
data/E.coli_iJR904.rda
data/E.coli_textbook.rda
data/Glycolysis.rda
data/H.pylori_ilT341.rda
data/H.sapiens_Recon_1.rda
data/M.barkeri_iAF692.rda
data/M.tuberculosis_iNJ661.rda
data/P.putida_iJN746.rda
data/Recon2.rda
data/S.aureus_iSB619.rda
data/S.cerevisiae_iND750.rda
data/datalist
data/lying.tunell.data.rda
inst
inst/CITATION
inst/COPYRIGHTS
inst/NEWS.Rd
inst/doc
inst/doc/BiGGR.R
inst/doc/BiGGR.Rnw
inst/doc/BiGGR.pdf
inst/extdata
inst/extdata/Gene_Symbol_Entrez_Foldchanges.csv
inst/extdata/Glycolysis.LIM
inst/extdata/Glycolysis_TCA.LIM
inst/extdata/Glycolysis_TCA_recon1_reactionIDs.txt
inst/extdata/Glycolysis_TCA_recon2_reactionIDs.txt
inst/extdata/Reactions.txt
inst/extdata/brainmodel_reactions.txt
man
man/BiGGR-internal.Rd
man/BiGGR-package.Rd
man/E.coli_iAF1260.Rd
man/E.coli_iJR904.Rd
man/E.coli_textbook.Rd
man/Glycolysis.Rd
man/H.pylori_ilT341.Rd
man/H.sapiens_Recon1.Rd
man/M.barkeri_iAF692.Rd
man/M.tuberculosis_iNJ661.Rd
man/P.putida_iJN746.Rd
man/Recon2.Rd
man/S.aureus_iSB619.Rd
man/S.cerevisiae_iND750.Rd
man/buildSBMLFromBiGG.Rd
man/buildSBMLFromGenes.Rd
man/buildSBMLFromPathways.Rd
man/buildSBMLFromReactionIDs.Rd
man/createLIMFromBiGG.Rd
man/createLIMFromSBML.Rd
man/extractGeneAssociations.Rd
man/extractPathways.Rd
man/getPathwaysForSBML.Rd
man/getRates.Rd
man/gprMapping.Rd
man/gprMappingAvg.Rd
man/lying.tunell.data.Rd
man/rmvSpliceVariant.Rd
man/sampleFluxEnsemble.Rd
man/sbml2hyperdraw.Rd
vignettes
vignettes/BiGGR.Rnw
vignettes/BiGGR.bib
BiGGR documentation built on May 20, 2017, 9:12 p.m.

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