sRACIPE: sRACIPE: A package for stochastic random circuit...

In lusystemsbio/sRACIPE: Systems biology tool to simulate gene regulatory circuits

sRACIPE: A package for stochastic random circuit perturbation.

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

sracipeSimulate Primary function to simulate a circuit. Contains options for plotting as well. sracipeKnockDown In-silico knockdown analysis of the circuit. Plots the relative changes in different cluster proportions.

sracipeOverExp In-silico over expression analysis of the circuit. Plots the relative changes in different cluster proportions.

sracipePlotData 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.

sracipeSimulate, sracipeKnockDown, sracipeOverExp, sracipePlotData

Author(s)

Maintainer: Mingyang Lu [e-mail] (ORCID)

Authors:

• Vivek Kohar

• Aidan Tillman

• Daniel Ramirez

See Also

Useful links:

• https://github.com/lusystemsbio/sRACIPE

• https://geneex.jax.org/

• https://vivekkohar.github.io/sRACIPE/

lusystemsbio/sRACIPE documentation built on Dec. 9, 2024, 8:25 a.m.