sRACIPE: sRACIPE: A package for stochastic random circuit...
In TheJacksonLaboratory/sRACIPE_dev: Systems biology tool to simulate gene regulatory circuits
Description
sRACIPE is a systems biology tool to study the role of noise and parameter
variation in gene regulatory circuits. It implements a randomization-based
method for gene circuit modeling. It allows us to study the effect of both
the gene expression noise and the parametric variation on any
gene regulatory circuit (GRC) using only its topology, and simulates an
ensemble of models with random kinetic parameters at multiple noise levels.
Statistical analysis of the generated gene expressions reveals the basin of
attraction and stability of various phenotypic states and their changes
associated with intrinsic and extrinsic noises. sRACIPE provides a holistic
picture to evaluate the effects of both the stochastic nature of cellular
processes and the parametric variation.
sRACIPE functions
simulateGRC
Primary function to simulate a circuit. Contains options for plotting as well.
knockdownAnalysis
In-silico knockdown analysis of the circuit. Plots the relative changes in
different cluster proportions.
overExprAnalysis
In-silico over expression analysis of the circuit.Plots the relative changes in
different cluster proportions.
plotData
Plot the simulated data. Includes options to plot the hierarchichal
clustering analysis, principal components, and uniform manifold
approximation and projection. Can plot the stochastic as well as the
knockout simulations.
calcHeatmapSimilarity
Compute the similarity between two datasets (experimental and simulated or
default simulations and perturbed simulations).
loadCircuit
Load a circuit
simulateGRC, knockdownAnalysis,
overExprAnalysis, plotData,
calcHeatmapSimilarity
TheJacksonLaboratory/sRACIPE_dev documentation built on May 7, 2019, 8:16 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description
sRACIPE is a systems biology tool to study the role of noise and parameter variation in gene regulatory circuits. It implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.
sRACIPE functions
simulateGRC
Primary function to simulate a circuit. Contains options for plotting as well.
knockdownAnalysis
In-silico knockdown analysis of the circuit. Plots the relative changes in
different cluster proportions.
overExprAnalysis
In-silico over expression analysis of the circuit.Plots the relative changes in
different cluster proportions.
plotData
Plot the simulated data. Includes options to plot the hierarchichal
clustering analysis, principal components, and uniform manifold
approximation and projection. Can plot the stochastic as well as the
knockout simulations.
calcHeatmapSimilarity
Compute the similarity between two datasets (experimental and simulated or
default simulations and perturbed simulations).
loadCircuit
Load a circuit
simulateGRC, knockdownAnalysis,
overExprAnalysis, plotData,
calcHeatmapSimilarity
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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