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

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.
check_julia	Check whether Julia is installed with correct version and all...
checkJuliaModules	Checking whether the required Julia modules are installed
checkJuliaVersion	Checks whether the installed version of Julia is at least a...
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
getComplexes	Retrieves regulatory complexes from in silico system
getEdges	Retrieves regulatory edges from in silico system
getGenes	Retrieve genes from in silico system
getGRN	Returns an igraph object (network) of the GRN of the in...
getJuliaEvaluator	Returns the current Julia evaluator.
getReactions	Retrieves the stochastic model for an in silico system
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.
installJuliaModules	Install required Julia modules
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.
plotGRNstatic	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.