Files in sybil
Efficient Constrained Based Modelling

inst
inst/CITATION
inst/NEWS.Rd
inst/extdata
inst/extdata/Ec_core_desc.tsv
inst/extdata/Ec_core_react.tsv
inst/extdata/Ec_core_met.tsv
inst/doc
inst/doc/sybil.R
inst/doc/sybil.Rnw
inst/doc/sybil.pdf
NAMESPACE
data
data/Ec_core.RData
R
R/validsysBiolAlg.R R/upgradeModelorg.R R/optObj_lpSolveAPIClass.R R/checkDefaultMethod.R R/deadEndMetabolite.R R/generateFluxdels.R R/makeLPcompatible.R R/readTSVmod.R R/doubleGeneDel.R R/sybilErrorClass.R R/optObj_lpSolveAPIcompat.R R/optsol_optimizeProbClass.R R/sysBiolAlgClass.R R/phpp.R R/sybilStack.R R/optsol_genedelClass.R R/checkEmptyField.R R/ppProcessing.R R/changeObjFunc.R R/sysBiolAlg_momaClass.R R/sysBiolAlg_lmomaClass.R R/parseBoolean.R R/changeBounds.R R/ceilValues.R R/validreactId_Exch.R R/sybilLogClass.R R/onlyChangeGPR.R R/createReactionString.R R/rmReact.R R/optObj_pointer.R R/mod2irrev.R R/modelorg_irrevClass.R R/validoptsol.R R/promptSysBiolAlg.R R/sysBiolAlg_fvClass.R R/robAna.R R/prepareSubSysMatrix.R R/generateModKey.R R/optObj_clpAPIClass.R R/singletonMetabolite.R R/reactId_ExchClass.R R/ypd.R R/addSolver.R R/modelorg2text.R R/generics.R R/checkAlgorithm.R R/reactIdClass.R R/optsol_fluxVarClass.R R/ppProcClass.R R/optsolClass.R R/optsol_blockedReactClass.R R/addExchReact.R R/geneDeletion.R R/progress.R R/optsol_robAnaClass.R R/checkReactId.R R/optsol_phppClass.R R/editEnvir.R R/blockedReact.R R/sysBiolAlg_mtfClass.R R/optObj_glpkAPIClass.R R/recodeMatrix.R R/netFluxClass.R R/settings.R R/floorValues.R R/addAlgorithm.R R/changeGPR.R R/doInRound.R R/oneFluxDel.R R/getsybilenv.R R/geneDel.R R/optObj_basicfunc.R R/summaryOptsolClass.R R/validmodelorg.R R/optObj_cplexAPIClass.R R/oneGeneDel.R R/modelorg2tsv.R R/optimizer.R R/doubleFluxDel.R R/sysBiolAlg_fbaEasyConstraintClass.R R/optsol_fluxdelClass.R R/sysBiolAlg_fbaClass.R R/fluxDistributionClass.R R/optObjClass.R R/sysBiolAlg_roomClass.R R/fluxVar.R R/modelorg2ExPA.R R/reassignFwBwMatch.R R/validreactId.R R/multiDel.R R/sysBiolAlg_mtfEasyConstraintClass.R R/check_brackets.R R/modelorgClass.R R/generateWT.R R/findExchReact.R R/printNamedList.R R/bracket_pairs.R R/zzz.R R/onlyCheckGPR.R R/checksolClass.R R/printLogComment.R R/doubleReact.R R/readTEXTmod.R R/addReact.R
vignettes
vignettes/sysBiolAlg-class.pdf vignettes/optObj-class.pdf
vignettes/sybil.bib
vignettes/optsol-class.pdf vignettes/sysBiolAlg-const.pdf vignettes/net-crop.pdf vignettes/sysBiolAlg-init.pdf
vignettes/sybil.Rnw
vignettes/optObj-const.pdf README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/optsol_genedel-class.Rd man/doubleGeneDel.Rd man/getsybilenv.Rd man/deadEndMetabolites-methods.Rd man/getNumCols-methods.Rd man/sysBiolAlg_fba-class.Rd man/robAna.Rd man/changeUptake-methods.Rd man/addExchReact.Rd man/getRowsUppBnds-methods.Rd man/addRowsToProb-methods.Rd man/resetChanges-methods.Rd man/solveLp-methods.Rd man/findExchReact.Rd man/addAlgorithm.Rd man/reactId_Exch-class.Rd man/changeRowsBnds-methods.Rd man/oneFluxDel.Rd man/deprecated.Rd man/optObj_lpSolveAPI-class.Rd man/optimizer.Rd man/promptSysBiolAlg.Rd man/changeMatrixRow-methods.Rd man/addRowsCols-methods.Rd man/checkDefaultMethod.Rd man/summaryOptsol-class.Rd man/geneDel.Rd man/blockedReact.Rd man/changeColsBnds-methods.Rd man/setObjDir-methods.Rd man/doubleReact.Rd man/changeGPR.Rd man/getRedCosts-methods.Rd man/optimizeProb-methods.Rd man/upgradeModelorg.Rd man/optsol_robAna-class.Rd man/printMetabolite-methods.Rd man/getFluxDist-methods.Rd man/getColPrim-methods.Rd man/loadQobj-methods.Rd man/getColsLowBnds-methods.Rd man/optObj_clpAPI-class.Rd man/phpp.Rd man/reactId-class.Rd man/changeBounds.Rd man/checkOptSol-methods.Rd man/fluxVar.Rd man/printReaction-methods.Rd man/netFlux-class.Rd man/getRowsNames-methods.Rd man/getObjCoefs-methods.Rd man/rmReact.Rd man/delProb-methods.Rd man/sybilStack.Rd man/setRowsNames-methods.Rd man/sysBiolAlg_moma-class.Rd man/onlyChangeGPR.Rd man/optsol_fluxdel-class.Rd man/changeColsBndsObjCoefs-methods.Rd man/optsol_phpp-class.Rd man/loadLPprob-methods.Rd man/sysBiolAlg_fbaEasyConstraint-class.Rd man/singletonMetabolites-methods.Rd man/optsol_blockedReact-class.Rd man/Ec_core.Rd man/sybilError-class.Rd man/getSolverParm-methods.Rd man/summaryOptsol.Rd man/readTSVmod.Rd man/modelorg2ExPA.Rd man/sybil-internal.Rd man/changeObjCoefs-methods.Rd man/geneDeletion.Rd man/addColsToProb-methods.Rd man/getNumRows-methods.Rd man/sybil-package.Rd man/sysBiolAlg_fv-class.Rd man/sysBiolAlg-class.Rd man/optObj_glpkAPI-class.Rd man/onlyCheckGPR.Rd man/addSolver.Rd man/scaleProb-methods.Rd man/ppProc-class.Rd man/readProb-methods.Rd man/getColsNames-methods.Rd man/getColsUppBnds-methods.Rd man/applyChanges-methods.Rd man/addCols-methods.Rd man/checkAkgorithm.Rd man/sysBiolAlg.Rd man/optObj_cplexAPI-class.Rd man/initProb-methods.Rd man/sysBiolAlg_mtf-class.Rd man/getSolStat-methods.Rd man/sensitivityAnalysis-methods.Rd man/checkVersion-methods.Rd man/sysBiolAlg_room-class.Rd man/optsol_fluxVar-class.Rd man/optsol_optimizeProb-class.Rd man/checkReactId.Rd man/optObj-class.Rd man/makeOptsolMO.Rd man/backupProb-methods.Rd man/getObjVal-methods.Rd man/addReact.Rd man/editEnvir.Rd man/getObjDir-methods.Rd man/addRows-methods.Rd man/modelorg-class.Rd man/changeObjFunc.Rd man/fluxDistribution-class.Rd man/modelorg2tsv.Rd man/writeProb-methods.Rd man/checksol-class.Rd man/oneGeneDel.Rd man/doubleFluxDel.Rd man/optsol-class.Rd man/mod2irrev.Rd man/sybilLog-class.Rd man/getRowsLowBnds-methods.Rd man/setColsNames-methods.Rd man/shrinkMatrix-methods.Rd man/SYBIL_SETTINGS.Rd man/setRhsZero-methods.Rd man/ypd.Rd man/getNumNnz-methods.Rd man/optObj.Rd man/modelorg_irrev-class.Rd man/sysBiolAlg_lmoma-class.Rd man/multiDel.Rd man/setSolverParm-methods.Rd
LICENSE
sybil documentation built on July 19, 2017, 5:02 p.m.