minval: MINimal VALidation for Stoichiometric Reactions

For a given set of stoichiometric reactions, this package evaluates the mass and charge balance, extracts all reactants, products, orphan metabolites, metabolite names and compartments. Also are included some options to write models in TSV and SBML formats.

Author
Daniel Osorio [aut,cre], Janneth Gonzalez [aut], Andres Pinzon-Velasco [aut].
Date of publication
2016-10-04 14:46:35
Maintainer
Daniel Osorio <dcosorioh@unal.edu.co>
License
GPL-2
Version
0.5

View on CRAN

Man pages

compartments
Extract the list of unique compartments for the metabolites...
convert2sbml
Write a model in a SBML format.
convert2sbmlR
Convert a data.frame data to a SBMLR object
getChEBI
Download the ChEBI database
isBalanced
Evaluate the mass or charge balance for a set of...
isValidSyntax
Evaluate if a stoichiometric reaction has a valid syntax
mapReactions
Return reactions from a reference data.frame by a selected...
metabolites
Identify the list of metabolites for a set of stoichiometric...
orphanProducts
Identify the orphan products of a set of stoichometric...
orphanReactants
Identify the orphan reactants of a set of stoichometric...
products
Identify the products of a stoichometric reaction
reactants
Identify the reactants of a stoichometric reaction
stoichiometricMatrix
Return the stoichiometric matrix for a set of stoichiometric...
writeTSVmod
Write a model in a TSV format for the 'sybil' R package.
xls2sbml
Write a model in SBML format from a XLS spreadsheet

Files in this package

minval
minval/inst
minval/inst/tests
minval/inst/tests/runit.compartments.R
minval/inst/tests/runalltest.R
minval/inst/tests/runit.orphanReactants.R
minval/inst/tests/runit.metabolites.R
minval/inst/tests/runit.isBalanced.R
minval/inst/tests/runit.reactants.R
minval/inst/tests/runit.products.R
minval/inst/tests/runit.isValidSyntax.R
minval/inst/tests/runit.orphanProducts.R
minval/inst/tests/runit.stoichiometricMatrix.R
minval/inst/extdata
minval/inst/extdata/glycolysisKEGG.xlsx
minval/inst/extdata/chemData.csv
minval/inst/extdata/glycolysisKEGG.csv
minval/tests
minval/tests/doRUnit.R
minval/NAMESPACE
minval/NEWS
minval/R
minval/R/getChEBI.R
minval/R/xls2sbml.R
minval/R/isBalanced.R
minval/R/orphanReactants.R
minval/R/orphanProducts.R
minval/R/stoichiometricMatrix.R
minval/R/metabolites.R
minval/R/compartments.R
minval/R/minvalInternal.R
minval/R/isValidSyntax.R
minval/R/convert2sbmlR.R
minval/R/products.R
minval/R/convert2sbml.R
minval/R/reactants.R
minval/R/mapReactions.R
minval/R/writeTSVmod.R
minval/README.md
minval/MD5
minval/DESCRIPTION
minval/man
minval/man/reactants.Rd
minval/man/metabolites.Rd
minval/man/convert2sbmlR.Rd
minval/man/products.Rd
minval/man/stoichiometricMatrix.Rd
minval/man/mapReactions.Rd
minval/man/writeTSVmod.Rd
minval/man/orphanReactants.Rd
minval/man/xls2sbml.Rd
minval/man/orphanProducts.Rd
minval/man/getChEBI.Rd
minval/man/convert2sbml.Rd
minval/man/compartments.Rd
minval/man/isBalanced.Rd
minval/man/isValidSyntax.Rd