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DESCRIPTION
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DESCRIPTION
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Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling
Version: 2.2.1
Date: 2022-10-12
Authors@R: c(
person("Mihail", "Anton", role = "cre", email = "[email protected]"),
person("Mayo", "Roettger", role = c("ctb"), email = "[email protected]"),
person("Gabriel", "Gelius-Dietrich", role = "aut"),
person(c("C.", "Jonathan"), "Fritzemeier", role = "ctb", email = "[email protected]"),
person("Rajen", "Piernikarczyk", role = "ctb"),
person(c("Marc", "Andre"), "Daxer", role = "ctb"),
person("Benjamin", "Braasch", role = "ctb"),
person("Abdelmoneim", "Desouki", role = "ctb"),
person(c("Martin", "J."), "Lercher", role = "ctb"))
Maintainer: Mihail Anton <[email protected]>
Depends: R (>= 3.2.0), Matrix, lattice
Imports: methods
Suggests: glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4),
lpSolveAPI (>= 5.5.2.0), parallel, grid
Additional_repositories: https://github.com/SysBioChalmers/cplexAPI, https://github.com/SysBioChalmers/clpAPI
URL:
https://www.cs.hhu.de/lehrstuehle-und-arbeitsgruppen/computational-cell-biology/software-contributions/sybil
Description: This Systems Biology Package (Gelius-Dietrich et. al. (2012) <doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.
LazyLoad: yes
License: GPL-3 | file LICENSE
Collate: generics.R validmodelorg.R validoptsol.R validreactId.R validreact.R
reactClass.R
validreactId_Exch.R validsysBiolAlg.R addAlgorithm.R
addExchReact.R addReact.R addSolver.R blockedReact.R
bracket_pairs.R ceilValues.R changeBounds.R changeGPR.R
changeObjFunc.R checkAlgorithm.R checkDefaultMethod.R
checkEmptyField.R checkReactId.R check_brackets.R
createReactionString.R deadEndMetabolite.R doInRound.R
doubleFluxDel.R doubleGeneDel.R doubleReact.R editEnvir.R
findExchReact.R floorValues.R fluxVar.R geneDel.R
geneDeletion.R generateFluxdels.R generateModKey.R generateWT.R
getsybilenv.R makeLPcompatible.R mod2irrev.R modelorg2ExPA.R
modelorg2text.R modelorg2tsv.R multiDel.R oneFluxDel.R
oneGeneDel.R onlyChangeGPR.R onlyCheckGPR.R optObj_basicfunc.R
optObj_lpSolveAPIcompat.R optimizer.R parseBoolean.R phpp.R
ppProcessing.R prepareSubSysMatrix.R printLogComment.R
printNamedList.R progress.R promptSysBiolAlg.R recodeMatrix.R
readTEXTmod.R readTSVmod.R reassignFwBwMatch.R rmReact.R
robAna.R settings.R singletonMetabolite.R sybilStack.R ypd.R
zzz.R modelorgClass.R modelorg_irrevClass.R optObj_pointer.R
optObjClass.R optObj_clpAPIClass.R optObj_cplexAPIClass.R
optObj_glpkAPIClass.R optObj_lpSolveAPIClass.R
sybilErrorClass.R ppProcClass.R netFluxClass.R
fluxDistributionClass.R reactIdClass.R reactId_ExchClass.R
optsolClass.R optsol_blockedReactClass.R
optsol_optimizeProbClass.R optsol_fluxVarClass.R
optsol_fluxdelClass.R optsol_robAnaClass.R optsol_phppClass.R
optsol_genedelClass.R checksolClass.R summaryOptsolClass.R
sysBiolAlgClass.R sysBiolAlg_fbaClass.R
sysBiolAlg_fbaEasyConstraintClass.R sysBiolAlg_fvClass.R
sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R
sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R
mergeReact2Modelorg.R
Packaged: 2022-08-19 09:14:00 UTC; mayo
Author: Mihail Anton [cre],
Mayo Roettger [ctb],
Gabriel Gelius-Dietrich [aut],
C. Jonathan Fritzemeier [ctb],
Rajen Piernikarczyk [ctb],
Marc Andre Daxer [ctb],
Benjamin Braasch [ctb],
Abdelmoneim Desouki [ctb],
Martin J. Lercher [ctb]