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. |
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