Package: BiGGR 1.43.0

Anand K. Gavai

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.

Authors:Anand K. Gavai, Hannes Hettling

BiGGR_1.43.0.tar.gz
BiGGR_1.43.0.zip(r-4.5)BiGGR_1.43.0.zip(r-4.4)

BiGGR_1.43.0.tar.gz(r-4.5-noble)BiGGR_1.43.0.tar.gz(r-4.4-noble)
BiGGR_1.43.0.tgz(r-4.4-emscripten)
BiGGR.pdf |BiGGR.html✨
BiGGR/json (API)
NEWS

# Install 'BiGGR' in R:
install.packages('BiGGR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:BiGGR-1.41.0(bioc 3.20)BiGGR-1.40.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

systems biologypathwaynetworkgraphandnetworkvisualizationmetabolomics

4.06 score 58 scripts 288 downloads 15 exports 21 dependencies

Last updated 26 days agofrom:bac514a088. Checks:OK: 1 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024

Exports:buildSBMLFromBiGGbuildSBMLFromGenesbuildSBMLFromPathwaysbuildSBMLFromReactionIDscreateLIMFromBiGGcreateLIMFromSBMLextractGeneAssociationsextractPathwaysgetPathwaysForSBMLgetRatesgprMappinggprMappingAvgrmvSpliceVariantsampleFluxEnsemblesbml2hyperdraw

Dependencies:BiocGenericsclidiagramgluegraphhyperdrawhypergraphlifecycleLIMlimSolvelpSolvemagrittrMASSquadprogRgraphvizrlangrsbmlshapestringistringrvctrs

BiGGR

Rendered fromBiGGR.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2019-04-09
Started: 2013-12-25

Readme and manuals

Help Manual

Help pageTopics
Creates an interface to the BiGG database, provides a framework for simulation and produces flux graphsBiGGR-package BiGGR
Build an SBML model from a given reactions file obtained from the BiGG databasebuildSBMLFromBiGG
Build an SBML model for specific genes in a given databasebuildSBMLFromGenes
Build an SBML model for specific pathway(s) in a given databasebuildSBMLFromPathways
Build an SBML model for specific reactions in a given databasebuildSBMLFromReactionIDs
Create a LIM model object from a BiGG database filecreateLIMFromBiGG
Create a LIM model object from an SBML filecreateLIMFromSBML
Ecoli dataset with ORFs and thermodynamic informationE.coli_iAF1260
Ecoli genome-scale modelE.coli_iJR904
Ecoli dataset from the BiGG databaseE.coli_textbook
Extract informations on genes from a given databaseextractGeneAssociations
Extract all pathways from given databaseextractPathways
Extract all pathways from a database that are relevant for a given SBML modelgetPathwaysForSBML
Get Optimized RatesgetRates
Metabolic reconstruction of Glycolysis pathwayGlycolysis
GPR mappinggprMapping
GPR mapping ignoring AND & OR operatorsgprMappingAvg
H.pylori in silico genome-scale characterization of single and double deletion mutantsH.pylori_ilT341
Reconstruction of human metabolism from the BiGG databaseH.sapiens_Recon_1
Dataset of in vivo cerebral metabolite uptake and release rates in healthy humans (old subjects)lying.tunell.data
Metabolic reconstruction of M.barkeri from the BiGG databaseM.barkeri_iAF692
Metabolic reconstruction of M.tuberculosis from the BiGG databaseM.tuberculosis_iNJ661
Metabolic reconstruction of P.putida from the BiGG databaseP.putida_iJN746
Human metabolic reconstruction Recon2Recon2
Remove splicing variants from the database.rmvSpliceVariant
Metabolic reconstruction of S.aureus from the BiGG databaseS.aureus_iSB619
Metabolic reconstruction of S.cerevisiae from the BiGG databaseS.cerevisiae_iND750
Sample a posterior ensemble of feasible flux configurations within the precision limits of given fluxes.sampleFluxEnsemble
Returns a graph representation of an SBML modelsbml2hyperdraw