g2f: Find and Fill Gaps in Metabolic Networks

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For a given metabolic network, this package finds the gaps (metabolites not produced or not consumed in any other reaction), and fills it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database <http://www.genome.jp/kegg/> is available.

Author
Kelly Botero[aut,cre], Daniel Osorio[aut,cre], Janneth Gonzalez[aut], Andres Pinzon[aut].
Date of publication
2016-10-08 08:48:09
Maintainer
Daniel Osorio <dcosorioh@unal.edu.co>
License
GPL-2
Version
0.1

View on CRAN

Man pages

additionCost
Calculate the cost of addition of a stoichiometric reaction...
blockedReactions
Identify blocked reactions in a metabolic network
gapFill
Find and fill gaps in a metabolic network
getReference
Download all the set of gene-associated stoichiometric...

Files in this package

g2f
g2f/NAMESPACE
g2f/R
g2f/R/getReference.R
g2f/R/gapFill.R
g2f/R/additionCost.R
g2f/R/g2f.internal.R
g2f/R/blockedReactions.R
g2f/README.md
g2f/MD5
g2f/DESCRIPTION
g2f/man
g2f/man/blockedReactions.Rd
g2f/man/additionCost.Rd
g2f/man/gapFill.Rd
g2f/man/getReference.Rd