Package: BiGGR 1.41.0
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:
BiGGR_1.41.0.tar.gz
BiGGR_1.41.0.zip(r-4.5)BiGGR_1.41.0.zip(r-4.4)
BiGGR_1.41.0.tar.gz(r-4.5-noble)BiGGR_1.41.0.tar.gz(r-4.4-noble)
BiGGR_1.41.0.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')) |
- 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
- Glycolysis - Metabolic reconstruction of Glycolysis pathway
- 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
- 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
- S.aureus_iSB619 - Metabolic reconstruction of S.aureus from the BiGG database
- S.cerevisiae_iND750 - Metabolic reconstruction of S.cerevisiae from the BiGG database
- lying.tunell.data - Dataset of in vivo cerebral metabolite uptake and release rates in healthy humans
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
Last updated 5 months agofrom:7de164bc57. Checks:OK: 1 NOTE: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 01 2024 |
| R-4.5-win | NOTE | Oct 01 2024 |
| R-4.5-linux | NOTE | Oct 01 2024 |
| R-4.4-win | NOTE | Oct 01 2024 |
Exports:buildSBMLFromBiGGbuildSBMLFromGenesbuildSBMLFromPathwaysbuildSBMLFromReactionIDscreateLIMFromBiGGcreateLIMFromSBMLextractGeneAssociationsextractPathwaysgetPathwaysForSBMLgetRatesgprMappinggprMappingAvgrmvSpliceVariantsampleFluxEnsemblesbml2hyperdraw
Dependencies:BiocGenericsclidiagramgluegraphhyperdrawhypergraphlifecycleLIMlimSolvelpSolvemagrittrMASSquadprogRgraphvizrlangrsbmlshapestringistringrvctrs
