minval: MINimal VALidation for Stoichiometric Reactions
Version 0.7

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 characterize and write models in TSV and SBML formats.

Browse man pages Browse package API and functions Browse package files

AuthorDaniel Osorio [aut, cre], Janneth Gonzalez [aut, ths], Andres Pinzon [aut, ths]
Date of publication2017-05-23 04:27:43 UTC
MaintainerDaniel Osorio <dcosorioh@unal.edu.co>
LicenseGPL (>= 2)
Version0.7
URL https://github.com/gibbslab/minval
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("minval")

Man pages

characterizeReactions: Characterize stoichiometric reactions by compartments and...
checkBalance: Evaluate the mass or charge balance for a set of...
compartments: Extract the compartments associated to metabolites of a set...
downloadChEBI: Download the ChEBI database
metabolites: Identify the list of metabolites for a set of stoichiometric...
orphanMetabolites: Identify the orphan metabolites of a set of stoichiometric...
products: Identify the products of a stoichometric reaction
reactants: Identify the reactants of a stoichometric reaction
stoichiometricMatrix: Build the stoichiometric matrix for a set of stoichiometric...
validateSyntax: Evaluate if a stoichiometric reaction has a valid syntax
writeSBMLmod: Write a model in SBML format
writeTSVmod: Write a model in TSV format for the 'sybil' R package

Functions

characterizeReactions Man page Source code
checkBalance Man page Source code
coefficients Source code
compartments Man page Source code
convertData Source code
downloadChEBI Man page Source code
extractData Source code
getLeft Source code
getRight Source code
metabolites Man page Source code
orphanMetabolites Man page Source code
orphanProducts Man page Source code
orphanReactants Man page Source code
products Man page Source code
reactants Man page Source code
reactionType Source code
rearmReactions Source code
removeCoefficients Source code
removeComments Source code
removeCompartment Source code
removeSpaces Source code
splitFormula Source code
stoichiometricMatrix Man page Source code
validateData Source code
validateSyntax Man page Source code
writeSBMLmod Man page Source code
writeTSVmod Man page Source code

Files

inst
inst/extdata
inst/extdata/rRECON2.csv
inst/extdata/chemData.csv
inst/extdata/mRECON2.csv
inst/extdata/glycolysisModel.csv
inst/doc
inst/doc/characterizeReactions.Rmd
inst/doc/characterizeReactions.html
inst/doc/characterizeReactions.R
inst/doc/MINVALintroduction.R
inst/doc/MINVALintroduction.Rmd
inst/doc/MINVALintroduction.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test.reactants.R
tests/testthat/test.products.R
tests/testthat/test.compartments.R
tests/testthat/test.orphanReactants.R
tests/testthat/test.validateSyntax.R
tests/testthat/test.orphanMetabolites.R
tests/testthat/test.stoichiometricMatrix.R
tests/testthat/test.metabolites.R
tests/testthat/test.reactionType.R
tests/testthat/test.orphanProducts.R
tests/testthat/test.checkBalance.R
NAMESPACE
NEWS.md
R
R/validateSyntax.R
R/downloadChEBI.R
R/characterizeReactions.R
R/stoichiometricMatrix.R
R/metabolites.R
R/compartments.R
R/products.R
R/writeSBMLmod.R
R/checkBalance.R
R/internalFunctions.R
R/orphanMetabolites.R
R/reactants.R
R/writeTSVmod.R
vignettes
vignettes/characterizeReactions.Rmd
vignettes/MINVALintroduction.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/reactants.Rd
man/metabolites.Rd
man/checkBalance.Rd
man/products.Rd
man/characterizeReactions.Rd
man/downloadChEBI.Rd
man/stoichiometricMatrix.Rd
man/writeTSVmod.Rd
man/writeSBMLmod.Rd
man/compartments.Rd
man/validateSyntax.Rd
man/orphanMetabolites.Rd
minval documentation built on May 23, 2017, 9:07 a.m.