Simulation of in Silico Multi-Omic Networks


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Documentation for package ‘sismonr’ version 2.1.0

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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.