| addComplex | Adds a regulatory complex in the in silico system. |
| addEdge | Adds an edge in the in silico system's regulatory network. |
| addGene | Adds a gene in the in silico system. |
| callJuliaStochasticSimulation | Calls the Julia simulation function. |
| createEmptyMultiOmicNetwork | Creates an empty in silico system. |
| createGenes | Creates genes for the in silico system. |
| createIndividual | Creates an in silico individual. |
| createInSilicoPopulation | Creates a population of in silico individuals. |
| createInSilicoSystem | Creates an in silico system. |
| createMultiOmicNetwork | Creates an in silico system. |
| createRegulatoryNetwork | Creates an in silico regulatory network. |
| createStochSystem | Creates a stochastic system from an in silico system. |
| createVariants | Create variants for genes in the system. |
| df2list | Tranforms a data-frame into a list. |
| findJuliaNoError | Find a Julia executable |
| getGRN | Returns an igraph object (network) of the GRN of the in silico system. |
| getJuliaEvaluator | Returns the current Julia evaluator. |
| getRNAseqMatrix | Transforms a simulation time-point into RNA-seq-like data. |
| insilicoindividualargs | Constructor function for the 'insilicoindividualargs' class. |
| insilicosystemargs | Constructor function for the 'insilicosystemsargs' class. |
| mergeAlleleAbundance | Merge the different allelic versions of the molecules. |
| mergeComplexesAbundance | Merge the free and in-complex versions of molecules. |
| mergePTMAbundance | Merge the original and PTM versions of the proteins. |
| newJuliaEvaluator | Creates a new ready-to-use Julia evaluator. |
| plotGRN | Plots the GRN of the in silico system. |
| plotHeatMap | Plots the result of a simulation as a heatmap. |
| plotMutations | Plots the QTL effect coefficients of a population. |
| plotSimulation | Plots the result of a simulation. |
| removeComplex | Removes a regulatory complex from the in silico system. |
| removeEdge | Removes an edge from the in silico system. |
| removeJuliaEvaluator | Closes a Julia evaluator. |
| sampleLibrarySize | Samples the expected library size of individuals/samples |
| simulateInSilicoSystem | Simulates an in silico system. |
| simulateParallelInSilicoSystem | Simulates an in silico system in parallel. |
| sortComponents | Sort component names. |
| steadyStateAbundance | Computes the steady state abundance of a molecule. |
| summariseSimulation | Returns a summary data-frame of a simulation. |