Man pages for saezlab/CARNIVAL
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
| addPerturbationNodes | Introduces a perturbation node connecting periphery nodes... |
| checkCarnivalOptions | Checks options provided for CARNIVAL |
| checkData | Checks the input data for correctness. |
| checkOptionsValidity | Checks if provided option names are valid. |
| checkPriorKnowledgeNetwork | Checks prior knowledge network for correct format. |
| createInternalDataRepresentation | Creates internal data representation - variables for ILP... |
| defaultCbcSolveCarnivalOptions | Sets default CARNIVAL options for cbc. |
| defaultCplexCarnivalOptions | Sets default CARNIVAL options for cplex. |
| defaultCplexSpecificOptions | Sets default options from cplex documentation. |
| defaultLpSolveCarnivalOptions | Sets default CARNIVAL options for lpSolve. |
| generateLpFileCarnival | 'generateLpFileCarnival' |
| getOptionsList | Returns the list of options needed/supported for each solver. |
| getSupportedSolvers | Returns the list of supported solvers. |
| getSupportedSolversFunctions | Supported solvers functions to work with all solvers in a... |
| isInputValidCarnival | Checks validity of all inputs of CARNIVAL |
| parseCplexLog | Parses the cplex log file and reads some basic information. |
| prepareForCarnivalRun | Prepares ILP formulation and writes it to .lp file.... |
| preprocessPriorKnowledgeNetwork | Preprocesses prior knowledge network: correct nodes... |
| processSolution | Exports the solution matrix to the final solution. |
| prune_network | prune_network |
| readOptions | Reads options from json file. |
| runCARNIVAL | 'runCARNIVAL' |
| runFromLpCarnival | 'runCarnivalFromLp' |
| runInverseCarnival | 'runInverseCarnival' |
| runVanillaCarnival | 'runVanillaCarnival' |
| searchForCPLEXSolver | searchForCPLEXSolver |
| sendTaskToSolver | Executes the solve on the provided ILP formulation (in .lp... |
| setCarnivalOptions | Sets CARNIVAL options for the solver. |
| solveCarnival | Main CARNIVAL function to execute the full pipeline: 1)... |
| solveCarnivalFromLp | Sends the ILP formulation defined in .lp file to solver. Uses... |
| solveWithCbc | Executes cbc solver on provided .lp file. |
| solveWithGurobi | Executes gurobi solver on provided .lp file. |
| suggestedCbcSpecificOptions | Suggests cbc specific options. |
| suggestedCplexSpecificOptions | Suggests cplex specific options.s |
| testRunCplex | checks if the the cplexPath exists |
| writeCplexCommandFileFromJson | writeCplexCommandFileFromJson |
| writeParsedData | Saves all provided data together with generated variables for... |
