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.
createInSilicoPopulation
                        Creates a population of in silico individuals.
createInSilicoSystem    Creates an in silico system.
createIndividual        Creates an in silico individual.
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.
