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"' |