A B C D E F G H I L M N O P R S T U V W Y misc
| sybil-package | sybil - Efficient Constrained Based Modelling in R |
| addAlgorithm | Add a New Algorithm Name to sybil |
| addCols | Add Columns to an Optimization Problem |
| addCols-method | Add Columns to an Optimization Problem |
| addCols-methods | Add Columns to an Optimization Problem |
| addColsToProb | Add New Columns (Variables) to an Optimization Problem |
| addColsToProb-method | Add New Columns (Variables) 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 |
| addReact-method | Add/Change Reactions in a Model |
| addRows | Add Rows to an Optimization Problem |
| addRows-method | Add Rows to an Optimization Problem |
| addRows-methods | Add Rows to an Optimization Problem |
| addRowsCols | Add Rows and Columns to an Optimization Problem |
| addRowsCols-method | Add Rows and Columns to an Optimization Problem |
| addRowsCols-methods | Add Rows and Columns to an Optimization Problem |
| addRowsToProb | Add New Rows (Constraints) to an Optimization Problem |
| addRowsToProb-method | Add New Rows (Constraints) to an Optimization Problem |
| addRowsToProb-methods | Add New Rows (Constraints) to an Optimization Problem |
| addSolver | Add a New Mathematical Programming Solver to sybil |
| ALGORITHM | Set and Get sybil Parameters |
| algorithm | Class optsol |
| algorithm-method | Class optsol |
| algorithm-method | Class '"sysBiolAlg"' |
| algorithm<- | Class optsol |
| algorithm<--method | Class optsol |
| algorithm<--method | Class '"sysBiolAlg"' |
| alg_par | Class '"sysBiolAlg"' |
| alg_par-method | Class optsol |
| alg_par-method | Class '"sysBiolAlg"' |
| alg_par<- | Class '"sysBiolAlg"' |
| alg_par<--method | Class optsol |
| alg_par<--method | Class '"sysBiolAlg"' |
| allGenes | Structure of Class "modelorg" |
| allGenes-method | Structure of Class "modelorg" |
| allGenes<- | Structure of Class "modelorg" |
| allGenes<--method | Structure of Class "modelorg" |
| applyChanges | Generic Function to Apply Changes to Objects of Class sysBiolAlg |
| applyChanges-method | Generic Function to Apply Changes to Objects of Class sysBiolAlg |
| applyChanges-methods | Generic Function to Apply Changes to Objects of Class sysBiolAlg |
| backupProb | Copies a Problem Object to a New Problem Object |
| backupProb-method | Copies a Problem Object to a New Problem Object |
| backupProb-methods | Copies a Problem Object to a New Problem Object |
| blocked | Class '"optsol_blockedReact"' |
| blocked-method | Class '"optsol_blockedReact"' |
| blocked<- | Class '"optsol_blockedReact"' |
| blocked<--method | Class '"optsol_blockedReact"' |
| blockedReact | Find Blocked Reactions in a Metabolic Network |
| blReact | Class '"optsol_fluxVar"' |
| blReact-method | Class '"optsol_fluxVar"' |
| changeBounds | Change Variable Bounds in a Metabolic Network |
| changeColsBnds | Change Column (Variable) Bounds in the Optimization Problem |
| changeColsBnds-method | Change Column (Variable) Bounds in the Optimization Problem |
| changeColsBnds-methods | Change Column (Variable) Bounds in the Optimization Problem |
| changeColsBndsObjCoefs | Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem |
| changeColsBndsObjCoefs-method | Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem |
| changeColsBndsObjCoefs-methods | Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem |
| changeGPR | Check and Change the GPR Rules |
| changeMatrixRow | Change a Row in the Constraint Matrix of the Optimization Problem |
| changeMatrixRow-method | Change a Row in the Constraint Matrix of the Optimization Problem |
| changeMatrixRow-methods | Change a Row in the Constraint Matrix of the Optimization Problem |
| changeMaxObj | Class '"sysBiolAlg_mtf"' |
| changeMaxObj-method | Class '"sysBiolAlg_mtf"' |
| changeObjCoefs | Change Column (Variable) Objective Coefficients in the Optimization Problem |
| changeObjCoefs-method | Change Column (Variable) Objective Coefficients in the Optimization Problem |
| changeObjCoefs-methods | Change Column (Variable) Objective Coefficients in the Optimization Problem |
| changeObjFunc | Sets/changes the Objective Function |
| changeRowsBnds | Change Row Bounds in the Optimization Problem |
| changeRowsBnds-method | Change Row Bounds in the Optimization Problem |
| changeRowsBnds-methods | Change Row Bounds in the Optimization Problem |
| changeUptake | Change Uptake Reactions |
| changeUptake-method | Change Uptake Reactions |
| changeUptake-methods | Change Uptake Reactions |
| checkAlgorithm | Check Algorithm |
| checkDefaultMethod | Validate Solver and Method |
| checkOptSol | Summarized Information About an Object of Class Optsol |
| checkOptSol-method | Summarized Information About an Object of Class Optsol |
| checkOptSol-methods | Summarized Information About an Object of Class Optsol |
| checkReactId | Check if a Reaction Id is Valid |
| checksol | Structure of the Class "checksol" |
| checksol-class | Structure of the Class "checksol" |
| checkSolStat | Class '"optObj"' |
| checkStat | Class optsol |
| checkStat-method | Class optsol |
| checkVersion | checks Version of modelorg |
| checkVersion,modelorg | checks Version of modelorg |
| checkVersion-method | checks Version of modelorg |
| checkVersion-methods | checks Version of modelorg |
| chlb | Class '"optsol_fluxdel"' |
| chlb-method | Class '"optsol_fluxdel"' |
| chlb<- | Class '"optsol_fluxdel"' |
| chlb<--method | Class '"optsol_fluxdel"' |
| chub | Class '"optsol_fluxdel"' |
| chub-method | Class '"optsol_fluxdel"' |
| chub<- | Class '"optsol_fluxdel"' |
| chub<--method | Class '"optsol_fluxdel"' |
| clpPtr-class | Class '"optObj"' |
| cmd | Class '"ppProc"' |
| cmd-method | Class '"ppProc"' |
| cmd<- | Class '"ppProc"' |
| cmd<--method | Class '"ppProc"' |
| comp_attr | Structure of Class "modelorg" |
| comp_attr-method | Structure of Class "modelorg" |
| comp_attr<- | Structure of Class "modelorg" |
| comp_attr<--method | Structure of Class "modelorg" |
| cplexPointer-class | Class '"optObj"' |
| cplexPtr-class | Class '"optObj"' |
| ctrlfl | Class '"optsol_robAna"' |
| ctrlfl-method | Class '"optsol_phpp"' |
| ctrlfl-method | Class '"optsol_robAna"' |
| ctrlfl<- | Class '"optsol_robAna"' |
| ctrlfl<--method | Class '"optsol_phpp"' |
| ctrlfl<--method | Class '"optsol_robAna"' |
| ctrlr | Class '"optsol_robAna"' |
| ctrlr-method | Class '"optsol_robAna"' |
| ctrlr<- | Class '"optsol_robAna"' |
| ctrlr<--method | Class '"optsol_robAna"' |
| deadEndMetabolites | Identify Dead End Metabolites |
| deadEndMetabolites-method | Identify Dead End Metabolites |
| deadEndMetabolites-methods | Identify Dead End Metabolites |
| deleted | Class '"optsol_fluxdel"' |
| deleted-method | Class '"optsol_fluxdel"' |
| deleted-method | Class '"optsol_genedel"' |
| delProb | Free Memory Associated to the Pointer to the Problem Object |
| delProb-method | Free Memory Associated to the Pointer to the Problem Object |
| delProb-methods | Free Memory Associated to the Pointer to the Problem Object |
| dels | Class '"optsol_fluxdel"' |
| dels-method | Class '"optsol_fluxdel"' |
| dels<- | Class '"optsol_fluxdel"' |
| dels<--method | Class '"optsol_fluxdel"' |
| didFoot | Class '"sybilLog"' |
| didFoot-method | Class '"sybilLog"' |
| didFoot<- | Class '"sybilLog"' |
| didFoot<--method | Class '"sybilLog"' |
| dim-method | Structure of Class "modelorg" |
| dim-method | Class '"optObj"' |
| doubleFluxDel | Double Flux Deletion Experiment |
| doubleGeneDel | Double Gene Deletion Experiment |
| doubleReact | Identifies Identical Reactions |
| EasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"' |
| Ec_core | Escherichia coli Core Metabolic Model |
| editEnvir | Environment Editor for Metabolic Networks |
| emsg | Class '"sybilError"' |
| emsg-method | Class '"sybilError"' |
| emsg<- | Class '"sybilError"' |
| emsg<--method | Class '"sybilError"' |
| enum | Class '"sybilError"' |
| enum-method | Class '"sybilError"' |
| enum<- | Class '"sybilError"' |
| enum<--method | Class '"sybilError"' |
| exit_code | Structure of the Class "checksol" |
| exit_code-method | Structure of the Class "checksol" |
| exit_code<- | Structure of the Class "checksol" |
| exit_code<--method | Structure of the Class "checksol" |
| exit_meaning | Structure of the Class "checksol" |
| exit_meaning-method | Structure of the Class "checksol" |
| exit_meaning<- | Structure of the Class "checksol" |
| exit_meaning<--method | Structure of the Class "checksol" |
| exit_num | Structure of the Class "checksol" |
| exit_num-method | Structure of the Class "checksol" |
| exit_num<- | Structure of the Class "checksol" |
| exit_num<--method | Structure of the Class "checksol" |
| ex_met | Class '"summaryOptsol"' |
| ex_met-method | Class '"summaryOptsol"' |
| ex_val | Class '"summaryOptsol"' |
| ex_val-method | Class '"summaryOptsol"' |
| fba | Class '"sysBiolAlg_fba"' |
| fbaEasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"' |
| fenc | Class '"sybilLog"' |
| fenc-method | Class '"sybilLog"' |
| fenc<- | Class '"sybilLog"' |
| fenc<--method | Class '"sybilLog"' |
| fh | Class '"sybilLog"' |
| fh-method | Class '"sybilLog"' |
| fh<- | Class '"sybilLog"' |
| fh<--method | Class '"sybilLog"' |
| file-class | Class '"sybilLog"' |
| findExchReact | Find Exchange Reactions |
| fldind | Class optsol |
| fldind-method | Class optsol |
| fldind-method | Class '"sysBiolAlg"' |
| fldind<- | Class optsol |
| fldind<--method | Class optsol |
| fldind<--method | Class '"sysBiolAlg"' |
| fluxdels | Class '"optsol_genedel"' |
| fluxdels-method | Class '"optsol_genedel"' |
| fluxdels<- | Class '"optsol_genedel"' |
| fluxdels<--method | Class '"optsol_genedel"' |
| fluxdist | Class optsol |
| fluxdist-method | Class optsol |
| fluxdist<- | Class optsol |
| fluxdist<--method | Class optsol |
| fluxDistribution | Class '"fluxDistribution"' |
| fluxDistribution-class | Class '"fluxDistribution"' |
| fluxes | Class optsol |
| fluxes-method | Class '"fluxDistribution"' |
| fluxes-method | Class optsol |
| fluxes<- | Class optsol |
| fluxes<--method | Class '"fluxDistribution"' |
| fluxes<--method | Class optsol |
| fluxVar | Flux Variability Analysis |
| fname | Class '"sybilLog"' |
| fname-method | Class '"sybilLog"' |
| fname<- | Class '"sybilLog"' |
| fname<--method | Class '"sybilLog"' |
| fpath | Class '"sybilLog"' |
| fpath-method | Class '"sybilLog"' |
| fpath<- | Class '"sybilLog"' |
| fpath<--method | Class '"sybilLog"' |
| fv | Class '"sysBiolAlg_fv"' |
| geneDel | Get Gene-Reaction Association |
| geneDeletion | Gene Deletion Experiments |
| genes | Structure of Class "modelorg" |
| genes-method | Structure of Class "modelorg" |
| genes<- | Structure of Class "modelorg" |
| genes<--method | Structure of Class "modelorg" |
| getColPrim | Get Primal Value of Variables After Optimization |
| getColPrim-method | Get Primal Value of Variables After Optimization |
| getColPrim-methods | Get Primal Value of Variables After Optimization |
| getColsLowBnds | Get Lower Bounds of the Columns (Variables) of the Optimization Problem |
| getColsLowBnds-method | Get Lower Bounds of the Columns (Variables) of the Optimization Problem |
| getColsLowBnds-methods | Get Lower Bounds of the Columns (Variables) of the Optimization Problem |
| getColsNames | Retrieve Variable Names |
| getColsNames-method | Retrieve Variable Names |
| getColsNames-methods | Retrieve Variable Names |
| getColsUppBnds | Get Upper Bounds of the Columns (Variables) of the Optimization Problem |
| getColsUppBnds-method | Get Upper Bounds of the Columns (Variables) of the Optimization Problem |
| getColsUppBnds-methods | Get Upper Bounds of the Columns (Variables) of the Optimization Problem |
| getFluxDist | Retrieve Flux Distribution |
| getFluxDist-method | Retrieve Flux Distribution |
| getFluxDist-methods | Retrieve Flux Distribution |
| getMeanReturn | Class '"optObj"' |
| getMeanStatus | Class '"optObj"' |
| getNetFlux | Class '"netFlux"' |
| getNumCols | Get Number of Columns (Variables) of the Optimization Problem |
| getNumCols-method | Get Number of Columns (Variables) of the Optimization Problem |
| getNumCols-methods | Get Number of Columns (Variables) of the Optimization Problem |
| getNumNnz | Retrieve the Number of Non-Zero Elements of the Constraint Matrix |
| getNumNnz-method | Retrieve the Number of Non-Zero Elements of the Constraint Matrix |
| getNumNnz-methods | Retrieve the Number of Non-Zero Elements of the Constraint Matrix |
| getNumRows | Get Number of Rows (Constraints) of the Optimization Problem |
| getNumRows-method | Get Number of Rows (Constraints) of the Optimization Problem |
| getNumRows-methods | Get Number of Rows (Constraints) of the Optimization Problem |
| getObjCoefs | Get Objective Coefficients of the Optimization Problem |
| getObjCoefs-method | Get Objective Coefficients of the Optimization Problem |
| getObjCoefs-methods | Get Objective Coefficients of the Optimization Problem |
| getObjDir | Get Direction of Optimization. |
| getObjDir-method | Get Direction of Optimization. |
| getObjDir-methods | Get Direction of Optimization. |
| getObjVal | Get Value of the Objective Function After Optimization |
| getObjVal-method | Get Value of the Objective Function After Optimization |
| getObjVal-methods | Get Value of the Objective Function After Optimization |
| getReaction | Functions to subset and merge modelorg objects. |
| getReaction-method | Functions to subset and merge modelorg objects. |
| getRedCosts | Get Reduced Costs of all Variables After Optimization |
| getRedCosts-method | Get Reduced Costs of all Variables After Optimization |
| getRedCosts-method | Class '"optsol_phpp"' |
| getRedCosts-methods | Get Reduced Costs of all Variables After Optimization |
| getRowsLowBnds | Get Lower Bounds of the Rows (Constraints) of the Optimization Problem |
| getRowsLowBnds-method | Get Lower Bounds of the Rows (Constraints) of the Optimization Problem |
| getRowsLowBnds-methods | Get Lower Bounds of the Rows (Constraints) of the Optimization Problem |
| getRowsNames | Retrieve Constraint Names |
| getRowsNames-method | Retrieve Constraint Names |
| getRowsNames-methods | Retrieve Constraint Names |
| getRowsUppBnds | Get Upper Bounds of the Rows (Constraints) of the Optimization Problem |
| getRowsUppBnds-method | Get Upper Bounds of the Rows (Constraints) of the Optimization Problem |
| getRowsUppBnds-methods | Get Upper Bounds of the Rows (Constraints) of the Optimization Problem |
| getSolStat | Get Solution Status After Optimization |
| getSolStat-method | Get Solution Status After Optimization |
| getSolStat-methods | Get Solution Status After Optimization |
| getSolverParm | Retrieve Current Parameter Settings Used By The Optimization Software |
| getSolverParm-method | Retrieve Current Parameter Settings Used By The Optimization Software |
| getSolverParm-methods | Retrieve Current Parameter Settings Used By The Optimization Software |
| getsybilenv | Print sybil Environment |
| glpkPtr-class | Class '"optObj"' |
| gpr | Structure of Class "modelorg" |
| gpr-method | Structure of Class "modelorg" |
| gpr<- | Structure of Class "modelorg" |
| gpr<--method | Structure of Class "modelorg" |
| gprRule | Structure of Class "modelorg" |
| gprRule-method | Structure of Class "modelorg" |
| gprRule<- | Structure of Class "modelorg" |
| gprRule<--method | Structure of Class "modelorg" |
| gprRules | Structure of Class "modelorg" |
| gprRules-method | Structure of Class "modelorg" |
| gprRules<- | Structure of Class "modelorg" |
| gprRules<--method | Structure of Class "modelorg" |
| hasEffect | Class '"optsol_genedel"' |
| hasEffect-method | Class '"optsol_genedel"' |
| hasEffect<- | Class '"optsol_genedel"' |
| hasEffect<--method | Class '"optsol_genedel"' |
| image-method | Class '"summaryOptsol"' |
| ind | Class '"ppProc"' |
| ind-method | Class '"ppProc"' |
| ind<- | Class '"ppProc"' |
| ind<--method | Class '"ppProc"' |
| initProb | Initialize Problem Object |
| initProb-method | Initialize Problem Object |
| initProb-methods | Initialize Problem Object |
| irrev | Class for Metabolic Networks in Irreversible Format. |
| irrev-method | Class for Metabolic Networks in Irreversible Format. |
| irrev2rev | Class for Metabolic Networks in Irreversible Format. |
| irrev2rev-method | Class for Metabolic Networks in Irreversible Format. |
| irrev2rev<- | Class for Metabolic Networks in Irreversible Format. |
| irrev2rev<--method | Class for Metabolic Networks in Irreversible Format. |
| irrev<- | Class for Metabolic Networks in Irreversible Format. |
| irrev<--method | Class for Metabolic Networks in Irreversible Format. |
| length-method | Class '"netFlux"' |
| length-method | Class optsol |
| length-method | Structure of Class "reactId" |
| lethal | Class '"optsol_fluxdel"' |
| lethal-method | Class '"optsol_fluxdel"' |
| lmoma | Class '"sysBiolAlg_lmoma"' |
| loadLPprob | Load Data to Optimization Problem |
| loadLPprob-method | Load Data to Optimization Problem |
| loadLPprob-methods | Load Data to Optimization Problem |
| loadMatrixPerColumnLPSOLVE | Class '"optObj_lpSolveAPI"' |
| loadQobj | Load Quadratic Part of the Objective Function to the Optimization Problem |
| loadQobj-method | Load Quadratic Part of the Objective Function to the Optimization Problem |
| loadQobj-methods | Load Quadratic Part of the Objective Function to the Optimization Problem |
| logCall | Class '"sybilLog"' |
| logCall-method | Class '"sybilLog"' |
| logClose<- | Class '"sybilLog"' |
| logClose<--method | Class '"sybilLog"' |
| logComment | Class '"sybilLog"' |
| logComment-method | Class '"sybilLog"' |
| logError | Class '"sybilLog"' |
| logError-method | Class '"sybilLog"' |
| logFH | Class '"sybilLog"' |
| logFH-method | Class '"sybilLog"' |
| logFileFH | Class '"sybilLog"' |
| logFoot<- | Class '"sybilLog"' |
| logFoot<--method | Class '"sybilLog"' |
| logHead | Class '"sybilLog"' |
| logHead-method | Class '"sybilLog"' |
| loglevel | Class '"sybilLog"' |
| loglevel-method | Class '"sybilLog"' |
| loglevel<- | Class '"sybilLog"' |
| loglevel<--method | Class '"sybilLog"' |
| logMessage | Class '"sybilLog"' |
| logMessage-method | Class '"sybilLog"' |
| logOptimization | Class '"sybilLog"' |
| logOptimization-method | Class '"sybilLog"' |
| logOptimizationTH | Class '"sybilLog"' |
| logOptimizationTH-method | Class '"sybilLog"' |
| logStep<- | Class '"sybilLog"' |
| logStep<--method | Class '"sybilLog"' |
| logWarning | Class '"sybilLog"' |
| logWarning-method | Class '"sybilLog"' |
| lowbnd | Structure of Class "modelorg" |
| lowbnd-method | Structure of Class "modelorg" |
| lowbnd-method | Class '"reactId_Exch"' |
| lowbnd<- | Structure of Class "modelorg" |
| lowbnd<--method | Structure of Class "modelorg" |
| lowbnd<--method | Class '"reactId_Exch"' |
| lpExtPtr-class | Class '"optObj"' |
| lp_dir | Class optsol |
| lp_dir-method | Class optsol |
| lp_dir<- | Class optsol |
| lp_dir<--method | Class optsol |
| lp_num_cols | Class optsol |
| lp_num_cols-method | Class optsol |
| lp_num_cols<- | Class optsol |
| lp_num_cols<--method | Class optsol |
| lp_num_rows | Class optsol |
| lp_num_rows-method | Class optsol |
| lp_num_rows<- | Class optsol |
| lp_num_rows<--method | Class optsol |
| lp_obj | Class optsol |
| lp_obj-method | Class optsol |
| lp_obj<- | Class optsol |
| lp_obj<--method | Class optsol |
| lp_ok | Class optsol |
| lp_ok-method | Class optsol |
| lp_ok<- | Class optsol |
| lp_ok<--method | Class optsol |
| lp_stat | Class optsol |
| lp_stat-method | Class optsol |
| lp_stat<- | Class optsol |
| lp_stat<--method | Class optsol |
| lstname | Class '"sybilLog"' |
| lstname-method | Class '"sybilLog"' |
| makeOptsolMO | Constructor Function for Objects of Class 'optsol_optimizeProb'. |
| matchrev | Class for Metabolic Networks in Irreversible Format. |
| matchrev-method | Class for Metabolic Networks in Irreversible Format. |
| matchrev<- | Class for Metabolic Networks in Irreversible Format. |
| matchrev<--method | Class for Metabolic Networks in Irreversible Format. |
| MAXIMUM | Set and Get sybil Parameters |
| maxSol | Class '"optsol_blockedReact"' |
| maxSol-method | Class '"optsol_blockedReact"' |
| maxSol-method | Class '"optsol_fluxVar"' |
| mergeReact2Modelorg | Functions to subset and merge modelorg objects. |
| METHOD | Set and Get sybil Parameters |
| method | Class optsol |
| method-method | Class '"optObj"' |
| method-method | Class optsol |
| method<- | Class optsol |
| method<--method | Class optsol |
| met_attr | Structure of Class "modelorg" |
| met_attr-method | Structure of Class "modelorg" |
| met_attr<- | Structure of Class "modelorg" |
| met_attr<--method | Structure of Class "modelorg" |
| met_comp | Structure of Class "modelorg" |
| met_comp-method | Structure of Class "modelorg" |
| met_comp<- | Structure of Class "modelorg" |
| met_comp<--method | Structure of Class "modelorg" |
| met_de | Structure of Class "modelorg" |
| met_de-method | Structure of Class "modelorg" |
| met_de<- | Structure of Class "modelorg" |
| met_de<--method | Structure of Class "modelorg" |
| met_id | Structure of Class "modelorg" |
| met_id-method | Structure of Class "modelorg" |
| met_id-method | Class '"reactId_Exch"' |
| met_id<- | Structure of Class "modelorg" |
| met_id<--method | Structure of Class "modelorg" |
| met_id<--method | Class '"reactId_Exch"' |
| met_name | Structure of Class "modelorg" |
| met_name-method | Structure of Class "modelorg" |
| met_name<- | Structure of Class "modelorg" |
| met_name<--method | Structure of Class "modelorg" |
| met_num | Structure of Class "modelorg" |
| met_num-method | Structure of Class "modelorg" |
| met_num<- | Structure of Class "modelorg" |
| met_num<--method | Structure of Class "modelorg" |
| met_pos | Class '"reactId_Exch"' |
| met_pos-method | Class '"reactId_Exch"' |
| met_pos<- | Class '"reactId_Exch"' |
| met_pos<--method | Class '"reactId_Exch"' |
| met_single | Structure of Class "modelorg" |
| met_single-method | Structure of Class "modelorg" |
| met_single<- | Structure of Class "modelorg" |
| met_single<--method | Structure of Class "modelorg" |
| minSol | Class '"optsol_blockedReact"' |
| minSol-method | Class '"optsol_blockedReact"' |
| minSol-method | Class '"optsol_fluxVar"' |
| mod2irrev | Produces a Model in Irreversible Format |
| modelorg | Structure of Class "modelorg" |
| modelorg-class | Structure of Class "modelorg" |
| modelorg2ExPA | Write an Instance of Class modelorg to File in ExPA Format |
| modelorg2tsv | Write an Instance of Class modelorg to File |
| modelorg_irrev | Class for Metabolic Networks in Irreversible Format. |
| modelorg_irrev-class | Class for Metabolic Networks in Irreversible Format. |
| mod_attr | Structure of Class "modelorg" |
| mod_attr-method | Structure of Class "modelorg" |
| mod_attr<- | Structure of Class "modelorg" |
| mod_attr<--method | Structure of Class "modelorg" |
| mod_compart | Structure of Class "modelorg" |
| mod_compart-method | Structure of Class "modelorg" |
| mod_compart<- | Structure of Class "modelorg" |
| mod_compart<--method | Structure of Class "modelorg" |
| mod_desc | Structure of Class "modelorg" |
| mod_desc-method | Structure of Class "modelorg" |
| mod_desc<- | Structure of Class "modelorg" |
| mod_desc<--method | Structure of Class "modelorg" |
| mod_id | Structure of Class "modelorg" |
| mod_id-method | Structure of Class "modelorg" |
| mod_id-method | Class optsol |
| mod_id-method | Structure of Class "reactId" |
| mod_id-method | Class '"summaryOptsol"' |
| mod_id<- | Structure of Class "modelorg" |
| mod_id<--method | Structure of Class "modelorg" |
| mod_id<--method | Class optsol |
| mod_id<--method | Structure of Class "reactId" |
| mod_id<--method | Class '"summaryOptsol"' |
| mod_key | Structure of Class "modelorg" |
| mod_key-method | Structure of Class "modelorg" |
| mod_key-method | Class optsol |
| mod_key-method | Structure of Class "reactId" |
| mod_key-method | Class '"summaryOptsol"' |
| mod_key<- | Structure of Class "modelorg" |
| mod_key<--method | Structure of Class "modelorg" |
| mod_key<--method | Class optsol |
| mod_key<--method | Structure of Class "reactId" |
| mod_key<--method | Class '"summaryOptsol"' |
| mod_name | Structure of Class "modelorg" |
| mod_name-method | Structure of Class "modelorg" |
| mod_name<- | Structure of Class "modelorg" |
| mod_name<--method | Structure of Class "modelorg" |
| mod_obj | Class optsol |
| mod_obj-method | Class optsol |
| mod_obj-method | Class '"summaryOptsol"' |
| mod_obj<- | Class '"summaryOptsol"' |
| mod_obj<--method | Class '"summaryOptsol"' |
| moma | Class '"sysBiolAlg_moma"' |
| mtf | Class '"sysBiolAlg_mtf"' |
| mtfEasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"' |
| multiDel | Parallel Support for sybil |
| nc | Class '"sysBiolAlg"' |
| nc-method | Class '"sysBiolAlg"' |
| nc<- | Class '"sysBiolAlg"' |
| nc<--method | Class '"sysBiolAlg"' |
| netFlux | Class '"netFlux"' |
| netFlux-class | Class '"netFlux"' |
| nfluxes | Class optsol |
| nfluxes-method | Class optsol |
| nnzero-method | Class '"fluxDistribution"' |
| nnzero-method | Class '"summaryOptsol"' |
| nr | Class '"sysBiolAlg"' |
| nr-method | Class '"sysBiolAlg"' |
| nr<- | Class '"sysBiolAlg"' |
| nr<--method | Class '"sysBiolAlg"' |
| num_of_fluxes | Class '"fluxDistribution"' |
| num_of_fluxes-method | Class '"fluxDistribution"' |
| num_of_prob | Class optsol |
| num_of_prob-method | Structure of the Class "checksol" |
| num_of_prob-method | Class optsol |
| num_of_prob<- | Class optsol |
| num_of_prob<--method | Structure of the Class "checksol" |
| num_of_prob<--method | Class optsol |
| nvar | Class '"fluxDistribution"' |
| nvar-method | Class '"fluxDistribution"' |
| nzeros | Class '"summaryOptsol"' |
| nzeros-method | Class '"summaryOptsol"' |
| obj_coef | Structure of Class "modelorg" |
| obj_coef-method | Structure of Class "modelorg" |
| obj_coef-method | Class optsol |
| obj_coef<- | Structure of Class "modelorg" |
| obj_coef<--method | Structure of Class "modelorg" |
| obj_coef<--method | Class optsol |
| obj_func | Class optsol |
| obj_func-method | Class optsol |
| obj_func<- | Class optsol |
| obj_func<--method | Class optsol |
| oneFluxDel | Single Flux Deletion Experiment |
| oneGeneDel | Single Gene Deletion Experiment |
| onlyChangeGPR | Change the GPR Rules |
| onlyCheckGPR | Check the GPR Rules |
| optimizeProb | Optimize Problem Object |
| optimizeProb-method | Optimize Problem Object |
| 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 | Class optsol |
| optsol-class | Class optsol |
| optsol_blockedReact-class | Class '"optsol_blockedReact"' |
| 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"' |
| OPT_DIRECTION | Set and Get sybil Parameters |
| pa | Class '"ppProc"' |
| pa-method | Class '"ppProc"' |
| pa<- | Class '"ppProc"' |
| pa<--method | Class '"ppProc"' |
| PATH_TO_MODEL | Set and Get sybil Parameters |
| phpp | Phenotypic Phase Plane Analysis |
| plot-method | Class '"fluxDistribution"' |
| plot-method | Class optsol |
| plot-method | Class '"optsol_fluxVar"' |
| plot-method | Class '"optsol_phpp"' |
| plot-method | Class '"optsol_robAna"' |
| plot-method | Class '"summaryOptsol"' |
| plotRangeVar | Class '"optsol_fluxVar"' |
| plotRangeVar-method | Class '"optsol_fluxVar"' |
| pointerToProb | Class '"optObj"' |
| pointerToProb-class | Class '"optObj"' |
| postProc | Class '"optsol_optimizeProb"' |
| postProc-method | Class '"optsol_optimizeProb"' |
| postProc<- | Class '"optsol_optimizeProb"' |
| postProc<--method | Class '"optsol_optimizeProb"' |
| ppProc | Class '"ppProc"' |
| ppProc-class | Class '"ppProc"' |
| preProc | Class '"optsol_optimizeProb"' |
| preProc-method | Class '"optsol_optimizeProb"' |
| preProc<- | Class '"optsol_optimizeProb"' |
| preProc<--method | Class '"optsol_optimizeProb"' |
| printExchange | Class '"summaryOptsol"' |
| printExchange-method | Class '"summaryOptsol"' |
| printMetabolite | Print Rows of the Stoichiometric Matrix |
| printMetabolite-method | Print Rows of the Stoichiometric Matrix |
| printMetabolite-methods | Print Rows of the Stoichiometric Matrix |
| printObjFunc | Structure of Class "modelorg" |
| printObjFunc-method | Structure of Class "modelorg" |
| printReaction | Print Columns of the Stoichiometric Matrix |
| printReaction-method | Print Columns of the Stoichiometric Matrix |
| printReaction-methods | Print Columns of the Stoichiometric Matrix |
| problem | Class '"sysBiolAlg"' |
| problem-method | Class '"sysBiolAlg"' |
| probType | Class '"optObj"' |
| probType-method | Class '"optObj"' |
| promptSysBiolAlg | Generate A Skeletal Structure of Subclasses of sysBiolAlg |
| rate | Class '"netFlux"' |
| rate-method | Class '"netFlux"' |
| react | Structure of Class "modelorg" |
| react-class | Structure of Class "modelorg" |
| react-method | Class '"optsol_blockedReact"' |
| react-method | Class '"optsol_fluxVar"' |
| react<- | Class '"optsol_blockedReact"' |
| react<--method | Class '"optsol_blockedReact"' |
| react<--method | Class '"optsol_fluxVar"' |
| reactId | Structure of Class "reactId" |
| reactId-class | Structure of Class "reactId" |
| reactId_Exch | Class '"reactId_Exch"' |
| reactId_Exch-class | Class '"reactId_Exch"' |
| react_attr | Structure of Class "modelorg" |
| react_attr-method | Structure of Class "modelorg" |
| react_attr<- | Structure of Class "modelorg" |
| react_attr<--method | Structure of Class "modelorg" |
| react_de | Structure of Class "modelorg" |
| react_de-method | Structure of Class "modelorg" |
| react_de<- | Structure of Class "modelorg" |
| react_de<--method | Structure of Class "modelorg" |
| react_id | Structure of Class "modelorg" |
| react_id-method | Structure of Class "modelorg" |
| react_id-method | Class '"netFlux"' |
| react_id-method | Class optsol |
| react_id-method | Structure of Class "reactId" |
| react_id<- | Structure of Class "modelorg" |
| react_id<--method | Structure of Class "modelorg" |
| react_id<--method | Class '"netFlux"' |
| react_id<--method | Class optsol |
| react_id<--method | Structure of Class "reactId" |
| react_name | Structure of Class "modelorg" |
| react_name-method | Structure of Class "modelorg" |
| react_name<- | Structure of Class "modelorg" |
| react_name<--method | Structure of Class "modelorg" |
| react_num | Structure of Class "modelorg" |
| react_num-method | Structure of Class "modelorg" |
| react_num<- | Structure of Class "modelorg" |
| react_num<--method | Structure of Class "modelorg" |
| react_pos | Structure of Class "reactId" |
| react_pos-method | Structure of Class "reactId" |
| react_pos<- | Structure of Class "reactId" |
| react_pos<--method | Structure of Class "reactId" |
| react_rev | Structure of Class "modelorg" |
| react_rev-method | Structure of Class "modelorg" |
| react_rev<- | Structure of Class "modelorg" |
| react_rev<--method | Structure of Class "modelorg" |
| react_single | Structure of Class "modelorg" |
| react_single-method | Structure of Class "modelorg" |
| react_single<- | Structure of Class "modelorg" |
| react_single<--method | Structure of Class "modelorg" |
| readProb | Read Problem Object From File |
| readProb-method | Read Problem Object From File |
| readProb-methods | Read Problem Object From File |
| readTSVmod | Read a Metabolic Network in a TSV (CSV) Format |
| resetChanges | Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg |
| resetChanges-method | Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg |
| resetChanges-methods | Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg |
| return_codeLPSOLVE | Class '"optObj_lpSolveAPI"' |
| rev2irrev | Class for Metabolic Networks in Irreversible Format. |
| rev2irrev-method | Class for Metabolic Networks in Irreversible Format. |
| rev2irrev<- | Class for Metabolic Networks in Irreversible Format. |
| rev2irrev<--method | Class for Metabolic Networks in Irreversible Format. |
| rmReact | Remove Reactions From a Model |
| robAna | Robustness Analysis |
| room | Class '"sysBiolAlg_room"' |
| rxnGeneMat | Structure of Class "modelorg" |
| rxnGeneMat-method | Structure of Class "modelorg" |
| rxnGeneMat<- | Structure of Class "modelorg" |
| rxnGeneMat<--method | Structure of Class "modelorg" |
| S | Structure of Class "modelorg" |
| s | Structure of Class "modelorg" |
| S-method | Structure of Class "modelorg" |
| s-method | Structure of Class "modelorg" |
| S<- | Structure of Class "modelorg" |
| s<- | Structure of Class "modelorg" |
| S<--method | Structure of Class "modelorg" |
| s<--method | Structure of Class "modelorg" |
| scaleProb | Scaling of the Constraint Matrix of an Optimization Problem |
| scaleProb-method | Scaling of the Constraint Matrix of an Optimization Problem |
| scaleProb-methods | Scaling of the Constraint Matrix of an Optimization Problem |
| sensitivityAnalysis | Sensitivity Analysis |
| sensitivityAnalysis-method | Sensitivity Analysis |
| sensitivityAnalysis-methods | Sensitivity Analysis |
| setColsNames | Set/Change Variable Names |
| setColsNames-method | Set/Change Variable Names |
| setColsNames-methods | Set/Change Variable Names |
| setObjDir | Set Direction of Optimization |
| setObjDir-method | Set Direction of Optimization |
| setObjDir-methods | Set Direction of Optimization |
| setRhsZero | Set Right Hand Side of the Optimization Problem To Zero |
| setRhsZero-method | Set Right Hand Side of the Optimization Problem To Zero |
| setRhsZero-methods | Set Right Hand Side of the Optimization Problem To Zero |
| setRowsNames | Set/Change Constraint Names |
| setRowsNames-method | Set/Change Constraint Names |
| setRowsNames-methods | Set/Change Constraint Names |
| setSolverParm | Set Parameters Used By The Optimization Software |
| setSolverParm-method | Set Parameters Used By The Optimization Software |
| setSolverParm-methods | Set Parameters Used By The Optimization Software |
| show-method | Structure of the Class "checksol" |
| show-method | Structure of Class "modelorg" |
| show-method | Class optsol |
| shrinkMatrix | Get a Subset of Matrix Like Objects |
| shrinkMatrix-method | Get a Subset of Matrix Like Objects |
| shrinkMatrix-methods | Get a Subset of Matrix Like Objects |
| singletonMetabolites | Identify Singleton Metabolites |
| singletonMetabolites-method | Identify Singleton Metabolites |
| singletonMetabolites-methods | Identify Singleton Metabolites |
| Snnz | Structure of Class "modelorg" |
| Snnz-method | Structure of Class "modelorg" |
| solveLp | Optimize Problem Object |
| solveLp-method | Optimize Problem Object |
| solveLp-methods | Optimize Problem Object |
| SOLVER | Set and Get sybil Parameters |
| solver | Class optsol |
| solver-method | Class '"optObj"' |
| solver-method | Class optsol |
| solver<- | Class optsol |
| solver<--method | Class optsol |
| SOLVER_CTRL_PARM | Set and Get sybil Parameters |
| status_code | Structure of the Class "checksol" |
| status_code-method | Structure of the Class "checksol" |
| status_code<- | Structure of the Class "checksol" |
| status_code<--method | Structure of the Class "checksol" |
| status_meaning | Structure of the Class "checksol" |
| status_meaning-method | Structure of the Class "checksol" |
| status_meaning<- | Structure of the Class "checksol" |
| status_meaning<--method | Structure of the Class "checksol" |
| status_num | Structure of the Class "checksol" |
| status_num-method | Structure of the Class "checksol" |
| status_num<- | Structure of the Class "checksol" |
| status_num<--method | Structure of the Class "checksol" |
| stclear | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stexists | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stfirst | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stinit | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stlength | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stlist | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stpop | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stpush | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stseek | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stshift | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| stunshift | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| subSys | Structure of Class "modelorg" |
| subSys-method | Structure of Class "modelorg" |
| subSys<- | Structure of Class "modelorg" |
| subSys<--method | Structure of Class "modelorg" |
| summaryOptsol | Summarize Objects of Class Optsol |
| summaryOptsol-class | Class '"summaryOptsol"' |
| sybil | sybil - Efficient Constrained Based Modelling in R |
| sybil-deprecated | Deprecated Functions and Methods in Package 'sybil' |
| sybilError | Class '"sybilError"' |
| sybilError-class | Class '"sybilError"' |
| sybilLog | Class '"sybilLog"' |
| sybilLog-class | Class '"sybilLog"' |
| sybilStack | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality |
| SYBIL_SETTINGS | Set and Get sybil Parameters |
| sysBiolAlg | General Constructor Function For Objects of Class 'sysBiolAlg' |
| sysBiolAlg-class | Class '"sysBiolAlg"' |
| sysBiolAlg_fba | Class '"sysBiolAlg_fba"' |
| sysBiolAlg_fba-class | Class '"sysBiolAlg_fba"' |
| sysBiolAlg_fbaEasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"' |
| sysBiolAlg_fbaEasyConstraint-class | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"' |
| sysBiolAlg_fv | Class '"sysBiolAlg_fv"' |
| sysBiolAlg_fv-class | Class '"sysBiolAlg_fv"' |
| sysBiolAlg_lmoma | Class '"sysBiolAlg_lmoma"' |
| sysBiolAlg_lmoma-class | Class '"sysBiolAlg_lmoma"' |
| sysBiolAlg_moma | Class '"sysBiolAlg_moma"' |
| sysBiolAlg_moma-class | Class '"sysBiolAlg_moma"' |
| sysBiolAlg_mtf | Class '"sysBiolAlg_mtf"' |
| sysBiolAlg_mtf-class | Class '"sysBiolAlg_mtf"' |
| sysBiolAlg_mtfEasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"' |
| sysBiolAlg_mtfEasyConstraint-class | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"' |
| sysBiolAlg_room | Class '"sysBiolAlg_room"' |
| sysBiolAlg_room-class | Class '"sysBiolAlg_room"' |
| TOLERANCE | Set and Get sybil Parameters |
| upgradeModelorg | Upgrade modelorg to newer version. |
| uppbnd | Structure of Class "modelorg" |
| uppbnd-method | Structure of Class "modelorg" |
| uppbnd-method | Class '"reactId_Exch"' |
| uppbnd<- | Structure of Class "modelorg" |
| uppbnd<--method | Structure of Class "modelorg" |
| uppbnd<--method | Class '"reactId_Exch"' |
| uptake | Class '"reactId_Exch"' |
| uptake-method | Class '"reactId_Exch"' |
| uptake<- | Class '"reactId_Exch"' |
| uptake<--method | Class '"reactId_Exch"' |
| uptMet | Class '"reactId_Exch"' |
| uptMet-method | Class '"reactId_Exch"' |
| uptReact | Class '"reactId_Exch"' |
| uptReact-method | Class '"reactId_Exch"' |
| USE_NAMES | Set and Get sybil Parameters |
| verblevel | Class '"sybilLog"' |
| verblevel-method | Class '"sybilLog"' |
| verblevel<- | Class '"sybilLog"' |
| verblevel<--method | Class '"sybilLog"' |
| version | Structure of Class "modelorg" |
| version-method | Structure of Class "modelorg" |
| version<- | Structure of Class "modelorg" |
| version<--method | Structure of Class "modelorg" |
| writeProb | Write Problem Object to File |
| writeProb-method | Write Problem Object to File |
| writeProb-methods | Write Problem Object to File |
| wrong_solver_msg | Class '"optObj"' |
| wrong_type_msg | Class '"optObj"' |
| ypd | In Sillico YPD Medium |
| [-method | Class '"fluxDistribution"' |
| [-method | Class '"optsol_fluxdel"' |
| [-method | Structure of Class "reactId" |
| [-method | Class '"reactId_Exch"' |