Files in sybil
Efficient Constrained Based Modelling
MD5
README.md
NAMESPACE
DESCRIPTION
LICENSE
R/optObjClass.R
R/sysBiolAlgClass.R
R/optsol_genedelClass.R
R/multiDel.R
R/deadEndMetabolite.R
R/modelorg2ExPA.R
R/ceilValues.R
R/readTEXTmod.R
R/checkDefaultMethod.R
R/doubleGeneDel.R
R/parseBoolean.R
R/sybilStack.R
R/prepareSubSysMatrix.R
R/progress.R
R/geneDel.R
R/optsol_fluxdelClass.R
R/onlyCheckGPR.R
R/recodeMatrix.R
R/sysBiolAlg_fbaClass.R
R/addSolver.R
R/check_brackets.R
R/optsol_fluxVarClass.R
R/modelorgClass.R
R/settings.R
R/upgradeModelorg.R
R/sysBiolAlg_fvClass.R
R/optsol_phppClass.R
R/changeBounds.R
R/generateModKey.R
R/optObj_glpkAPIClass.R
R/validmodelorg.R
R/sysBiolAlg_lmomaClass.R
R/onlyChangeGPR.R
R/optObj_pointer.R
R/modelorg_irrevClass.R
R/mergeReact2Modelorg.R
R/validreactId.R
R/oneGeneDel.R
R/sybilLogClass.R
R/optsolClass.R
R/sysBiolAlg_mtfClass.R
R/reactIdClass.R
R/reactClass.R
R/checksolClass.R
R/robAna.R
R/addAlgorithm.R
R/validoptsol.R
R/optsol_optimizeProbClass.R
R/reassignFwBwMatch.R
R/doInRound.R
R/checkAlgorithm.R
R/optObj_basicfunc.R
R/addExchReact.R
R/generateWT.R
R/doubleFluxDel.R
R/geneDeletion.R
R/sysBiolAlg_mtfEasyConstraintClass.R
R/optsol_robAnaClass.R
R/validreactId_Exch.R
R/readTSVmod.R
R/modelorg2tsv.R
R/ppProcessing.R
R/validsysBiolAlg.R
R/sysBiolAlg_roomClass.R
R/makeLPcompatible.R
R/fluxDistributionClass.R
R/checkReactId.R
R/createReactionString.R
R/generics.R
R/checkEmptyField.R
R/changeObjFunc.R
R/optObj_cplexAPIClass.R
R/ppProcClass.R
R/netFluxClass.R
R/findExchReact.R
R/ypd.R
R/changeGPR.R
R/sybilErrorClass.R
R/blockedReact.R
R/mod2irrev.R
R/phpp.R
R/optObj_lpSolveAPIClass.R
R/singletonMetabolite.R
R/printNamedList.R
R/getsybilenv.R
R/zzz.R
R/optimizer.R
R/validreact.R
R/promptSysBiolAlg.R
R/sysBiolAlg_fbaEasyConstraintClass.R
R/sysBiolAlg_momaClass.R
R/optsol_blockedReactClass.R
R/doubleReact.R
R/optObj_lpSolveAPIcompat.R
R/floorValues.R
R/oneFluxDel.R
R/editEnvir.R
R/generateFluxdels.R
R/bracket_pairs.R
R/modelorg2text.R
R/fluxVar.R
R/summaryOptsolClass.R
R/reactId_ExchClass.R
R/addReact.R
R/printLogComment.R
R/rmReact.R
R/optObj_clpAPIClass.R
inst/NEWS.Rd
inst/CITATION
inst/doc/sybil.pdf
inst/doc/sybil.Rnw
inst/doc/sybil.R
inst/extdata/Ec_core_met.tsv
inst/extdata/Ec_core_react.tsv
inst/extdata/Ec_core_desc.tsv
build/vignette.rds
vignettes/sybil.Rnw
vignettes/net-crop.pdf
vignettes/sysBiolAlg-class.pdf
vignettes/optsol-class.pdf
vignettes/sysBiolAlg-init.pdf
vignettes/optObj-class.pdf
vignettes/sysBiolAlg-const.pdf
vignettes/sybil.bib
vignettes/optObj-const.pdf
data/Ec_core.RData
man/deadEndMetabolites-methods.Rd
man/editEnvir.Rd
man/optsol_genedel-class.Rd
man/solveLp-methods.Rd
man/optsol_optimizeProb-class.Rd
man/checkReactId.Rd
man/sysBiolAlg_room-class.Rd
man/checkDefaultMethod.Rd
man/addAlgorithm.Rd
man/checksol-class.Rd
man/optimizer.Rd
man/setObjDir-methods.Rd
man/phpp.Rd
man/blockedReact.Rd
man/sysBiolAlg_fbaEasyConstraint-class.Rd
man/addRows-methods.Rd
man/optObj_lpSolveAPI-class.Rd
man/netFlux-class.Rd
man/getRowsLowBnds-methods.Rd
man/printMetabolite-methods.Rd
man/getNumCols-methods.Rd
man/addRowsCols-methods.Rd
man/geneDel.Rd
man/checkOptSol-methods.Rd
man/summaryOptsol.Rd
man/sybilStack.Rd
man/changeObjFunc.Rd
man/checkVersion-methods.Rd
man/getRowsNames-methods.Rd
man/getNumRows-methods.Rd
man/optObj-class.Rd
man/optsol_fluxVar-class.Rd
man/optsol_fluxdel-class.Rd
man/sybilError-class.Rd
man/doubleGeneDel.Rd
man/loadLPprob-methods.Rd
man/optsol_blockedReact-class.Rd
man/sybil-internal.Rd
man/getFluxDist-methods.Rd
man/onlyChangeGPR.Rd
man/modelorg-class.Rd
man/resetChanges-methods.Rd
man/sysBiolAlg_fba-class.Rd
man/getColsLowBnds-methods.Rd
man/getsybilenv.Rd
man/getNumNnz-methods.Rd
man/optsol_phpp-class.Rd
man/getObjDir-methods.Rd
man/sensitivityAnalysis-methods.Rd
man/sysBiolAlg-class.Rd
man/optimizeProb-methods.Rd
man/shrinkMatrix-methods.Rd
man/upgradeModelorg.Rd
man/scaleProb-methods.Rd
man/modelorg2ExPA.Rd
man/printReaction-methods.Rd
man/ppProc-class.Rd
man/changeRowsBnds-methods.Rd
man/addCols-methods.Rd
man/getSolverParm-methods.Rd
man/doubleReact.Rd
man/getRowsUppBnds-methods.Rd
man/changeBounds.Rd
man/addColsToProb-methods.Rd
man/makeOptsolMO.Rd
man/modelorg2tsv.Rd
man/summaryOptsol-class.Rd
man/mergeReact2Modelorg.Rd
man/modelorg_irrev-class.Rd
man/writeProb-methods.Rd
man/initProb-methods.Rd
man/optObj_cplexAPI-class.Rd
man/delProb-methods.Rd
man/getRedCosts-methods.Rd
man/setColsNames-methods.Rd
man/checkAkgorithm.Rd
man/setSolverParm-methods.Rd
man/getObjCoefs-methods.Rd
man/sysBiolAlg_lmoma-class.Rd
man/changeColsBnds-methods.Rd
man/addExchReact.Rd
man/fluxVar.Rd
man/loadQobj-methods.Rd
man/optObj_clpAPI-class.Rd
man/changeMatrixRow-methods.Rd
man/getColsUppBnds-methods.Rd
man/changeObjCoefs-methods.Rd
man/onlyCheckGPR.Rd
man/robAna.Rd
man/optsol-class.Rd
man/sysBiolAlg.Rd
man/readProb-methods.Rd
man/oneGeneDel.Rd
man/changeGPR.Rd
man/getColPrim-methods.Rd
man/singletonMetabolites-methods.Rd
man/applyChanges-methods.Rd
man/Ec_core.Rd
man/SYBIL_SETTINGS.Rd
man/rmReact.Rd
man/mod2irrev.Rd
man/deprecated.Rd
man/readTSVmod.Rd
man/backupProb-methods.Rd
man/geneDeletion.Rd
man/sysBiolAlg_mtf-class.Rd
man/oneFluxDel.Rd
man/getSolStat-methods.Rd
man/doubleFluxDel.Rd
man/optsol_robAna-class.Rd
man/optObj.Rd
man/addReact.Rd
man/addRowsToProb-methods.Rd
man/findExchReact.Rd
man/reactId-class.Rd
man/sybilLog-class.Rd
man/fluxDistribution-class.Rd
man/getObjVal-methods.Rd
man/sysBiolAlg_fv-class.Rd
man/multiDel.Rd
man/optObj_glpkAPI-class.Rd
man/setRowsNames-methods.Rd
man/setRhsZero-methods.Rd
man/changeUptake-methods.Rd
man/sysBiolAlg_moma-class.Rd
man/ypd.Rd
man/promptSysBiolAlg.Rd
man/reactId_Exch-class.Rd
man/sybil-package.Rd
man/getColsNames-methods.Rd
man/changeColsBndsObjCoefs-methods.Rd
man/addSolver.Rd
