Man pages for sismonr
Simulation of in Silico Multi-Omic Networks

addComplexAdds a regulatory complex in the in silico system.
addEdgeAdds an edge in the in silico system's regulatory network.
addGeneAdds a gene in the in silico system.
callJuliaStochasticSimulationCalls the Julia simulation function.
createEmptyMultiOmicNetworkCreates an empty in silico system.
createGenesCreates genes for the in silico system.
createIndividualCreates an in silico individual.
createInSilicoPopulationCreates a population of in silico individuals.
createInSilicoSystemCreates an in silico system.
createMultiOmicNetworkCreates an in silico system.
createRegulatoryNetworkCreates an in silico regulatory network.
createStochSystemCreates a stochastic system from an in silico system.
createVariantsCreate variants for genes in the system.
df2listTranforms a data-frame into a list.
findJuliaNoErrorFind a Julia executable
getGRNReturns an igraph object (network) of the GRN of the in...
getJuliaEvaluatorReturns the current Julia evaluator.
getRNAseqMatrixTransforms a simulation time-point into RNA-seq-like data.
insilicoindividualargsConstructor function for the 'insilicoindividualargs' class.
insilicosystemargsConstructor function for the 'insilicosystemsargs' class.
mergeAlleleAbundanceMerge the different allelic versions of the molecules.
mergeComplexesAbundanceMerge the free and in-complex versions of molecules.
mergePTMAbundanceMerge the original and PTM versions of the proteins.
newJuliaEvaluatorCreates a new ready-to-use Julia evaluator.
plotGRNPlots the GRN of the in silico system.
plotHeatMapPlots the result of a simulation as a heatmap.
plotMutationsPlots the QTL effect coefficients of a population.
plotSimulationPlots the result of a simulation.
removeComplexRemoves a regulatory complex from the in silico system.
removeEdgeRemoves an edge from the in silico system.
removeJuliaEvaluatorCloses a Julia evaluator.
sampleLibrarySizeSamples the expected library size of individuals/samples
simulateInSilicoSystemSimulates an in silico system.
simulateParallelInSilicoSystemSimulates an in silico system in parallel.
sortComponentsSort component names.
steadyStateAbundanceComputes the steady state abundance of a molecule.
summariseSimulationReturns a summary data-frame of a simulation.
sismonr documentation built on Feb. 11, 2020, 9:07 a.m.