Man pages for sybil
Efficient Constrained Based Modelling
| addAlgorithm | Add a New Algorithm Name to sybil |
| addCols-methods | Add Columns to an Optimization Problem |
| addColsToProb-methods | Add New Columns (Variables) to an Optimization Problem |
| addExchReact | Add Exchange Reactions to a Model |
| addReact | Add/Change Reactions in a Model |
| addRowsCols-methods | Add Rows and Columns to an Optimization Problem |
| addRows-methods | Add Rows to an Optimization Problem |
| addRowsToProb-methods | Add New Rows (Constraints) to an Optimization Problem |
| addSolver | Add a New Mathematical Programming Solver to sybil |
| applyChanges-methods | Generic Function to Apply Changes to Objects of Class... |
| backupProb-methods | Copies a Problem Object to a New Problem Object |
| blockedReact | Find Blocked Reactions in a Metabolic Network |
| changeBounds | Change Variable Bounds in a Metabolic Network |
| changeColsBnds-methods | Change Column (Variable) Bounds in the Optimization Problem |
| changeColsBndsObjCoefs-methods | Change Column (Variable) Bounds and Objective Coefficients in... |
| changeGPR | Check and Change the GPR Rules |
| changeMatrixRow-methods | Change a Row in the Constraint Matrix of the Optimization... |
| changeObjCoefs-methods | Change Column (Variable) Objective Coefficients in the... |
| changeObjFunc | Sets/changes the Objective Function |
| changeRowsBnds-methods | Change Row Bounds in the Optimization Problem |
| changeUptake-methods | Change Uptake Reactions |
| checkAkgorithm | Check Algorithm |
| checkDefaultMethod | Validate Solver and Method |
| checkOptSol-methods | Summarized Information About an Object of Class Optsol |
| checkReactId | Check if a Reaction Id is Valid |
| checksol-class | Structure of the Class "checksol" |
| checkVersion-methods | checks Version of modelorg |
| deadEndMetabolites-methods | Identify Dead End Metabolites |
| delProb-methods | Free Memory Associated to the Pointer to the Problem Object |
| deprecated | Deprecated Functions and Methods in Package 'sybil' |
| doubleFluxDel | Double Flux Deletion Experiment |
| doubleGeneDel | Double Gene Deletion Experiment |
| doubleReact | Identifies Identical Reactions |
| Ec_core | Escherichia coli Core Metabolic Model |
| editEnvir | Environment Editor for Metabolic Networks |
| findExchReact | Find Exchange Reactions |
| fluxDistribution-class | Class '"fluxDistribution"' |
| fluxVar | Flux Variability Analysis |
| geneDel | Get Gene-Reaction Association |
| geneDeletion | Gene Deletion Experiments |
| getColPrim-methods | Get Primal Value of Variables After Optimization |
| getColsLowBnds-methods | Get Lower Bounds of the Columns (Variables) of the... |
| getColsNames-methods | Retrieve Variable Names |
| getColsUppBnds-methods | Get Upper Bounds of the Columns (Variables) of the... |
| getFluxDist-methods | Retrieve Flux Distribution |
| getNumCols-methods | Get Number of Columns (Variables) of the Optimization Problem |
| getNumNnz-methods | Retrieve the Number of Non-Zero Elements of the Constraint... |
| getNumRows-methods | Get Number of Rows (Constraints) of the Optimization Problem |
| getObjCoefs-methods | Get Objective Coefficients of the Optimization Problem |
| getObjDir-methods | Get Direction of Optimization. |
| getObjVal-methods | Get Value of the Objective Function After Optimization |
| getRedCosts-methods | Get Reduced Costs of all Variables After Optimization |
| getRowsLowBnds-methods | Get Lower Bounds of the Rows (Constraints) of the... |
| getRowsNames-methods | Retrieve Constraint Names |
| getRowsUppBnds-methods | Get Upper Bounds of the Rows (Constraints) of the... |
| getSolStat-methods | Get Solution Status After Optimization |
| getSolverParm-methods | Retrieve Current Parameter Settings Used By The Optimization... |
| getsybilenv | Print sybil Environment |
| initProb-methods | Initialize Problem Object |
| loadLPprob-methods | Load Data to Optimization Problem |
| loadQobj-methods | Load Quadratic Part of the Objective Function to the... |
| makeOptsolMO | Constructor Function for Objects of Class... |
| mergeReact2Modelorg | Functions to subset and merge modelorg objects. |
| mod2irrev | Produces a Model in Irreversible Format |
| modelorg2ExPA | Write an Instance of Class modelorg to File in ExPA Format |
| modelorg2tsv | Write an Instance of Class modelorg to File |
| modelorg-class | Structure of Class "modelorg" |
| modelorg_irrev-class | Class for Metabolic Networks in Irreversible Format. |
| multiDel | Parallel Support for sybil |
| netFlux-class | Class '"netFlux"' |
| oneFluxDel | Single Flux Deletion Experiment |
| oneGeneDel | Single Gene Deletion Experiment |
| onlyChangeGPR | Change the GPR Rules |
| onlyCheckGPR | Check the GPR Rules |
| optimizeProb-methods | Optimize Problem Object |
| optimizer | Performs Series of Optimizations |
| optObj | General Constructor Function For Objects of Class 'optObj' |
| optObj-class | Class '"optObj"' |
| optObj_clpAPI-class | Class '"optObj_clpAPI"' |
| optObj_cplexAPI-class | Class '"optObj_cplexAPI"' |
| optObj_glpkAPI-class | Class '"optObj_glpkAPI"' |
| optObj_lpSolveAPI-class | Class '"optObj_lpSolveAPI"' |
| optsol_blockedReact-class | Class '"optsol_blockedReact"' |
| optsol-class | Class optsol |
| optsol_fluxdel-class | Class '"optsol_fluxdel"' |
| optsol_fluxVar-class | Class '"optsol_fluxVar"' |
| optsol_genedel-class | Class '"optsol_genedel"' |
| optsol_optimizeProb-class | Class '"optsol_optimizeProb"' |
| optsol_phpp-class | Class '"optsol_phpp"' |
| optsol_robAna-class | Class '"optsol_robAna"' |
| phpp | Phenotypic Phase Plane Analysis |
| ppProc-class | Class '"ppProc"' |
| printMetabolite-methods | Print Rows of the Stoichiometric Matrix |
| printReaction-methods | Print Columns of the Stoichiometric Matrix |
| promptSysBiolAlg | Generate A Skeletal Structure of Subclasses of sysBiolAlg |
| reactId-class | Structure of Class "reactId" |
| reactId_Exch-class | Class '"reactId_Exch"' |
| readProb-methods | Read Problem Object From File |
| readTSVmod | Read a Metabolic Network in a TSV (CSV) Format |
| resetChanges-methods | Generic Function to Reset Temporary Changes in Objects of... |
| rmReact | Remove Reactions From a Model |
| robAna | Robustness Analysis |
| scaleProb-methods | Scaling of the Constraint Matrix of an Optimization Problem |
| sensitivityAnalysis-methods | Sensitivity Analysis |
| setColsNames-methods | Set/Change Variable Names |
| setObjDir-methods | Set Direction of Optimization |
| setRhsZero-methods | Set Right Hand Side of the Optimization Problem To Zero |
| setRowsNames-methods | Set/Change Constraint Names |
| setSolverParm-methods | Set Parameters Used By The Optimization Software |
| shrinkMatrix-methods | Get a Subset of Matrix Like Objects |
| singletonMetabolites-methods | Identify Singleton Metabolites |
| solveLp-methods | Optimize Problem Object |
| summaryOptsol | Summarize Objects of Class Optsol |
| summaryOptsol-class | Class '"summaryOptsol"' |
| sybilError-class | Class '"sybilError"' |
| sybil-internal | Internal sybil Functions |
| sybilLog-class | Class '"sybilLog"' |
| sybil-package | sybil - Efficient Constrained Based Modelling in R |
| SYBIL_SETTINGS | Set and Get sybil Parameters |
| sybilStack | A Data Type Providing Stack (LIFO) And Queue (FIFO)... |
| sysBiolAlg | General Constructor Function For Objects of Class... |
| sysBiolAlg-class | Class '"sysBiolAlg"' |
| sysBiolAlg_fba-class | Class '"sysBiolAlg_fba"' |
| sysBiolAlg_fbaEasyConstraint-class | Class '"sysBiolAlg_fbaEasyConstraint"' and Class... |
| sysBiolAlg_fv-class | Class '"sysBiolAlg_fv"' |
| sysBiolAlg_lmoma-class | Class '"sysBiolAlg_lmoma"' |
| sysBiolAlg_moma-class | Class '"sysBiolAlg_moma"' |
| sysBiolAlg_mtf-class | Class '"sysBiolAlg_mtf"' |
| sysBiolAlg_room-class | Class '"sysBiolAlg_room"' |
| upgradeModelorg | Upgrade modelorg to newer version. |
| writeProb-methods | Write Problem Object to File |
| ypd | In Sillico YPD Medium |
