sRACIPE

DOI: 10.18129/B9.bioc.sRACIPE  

Systems biology tool to simulate gene regulatory circuits

Bioconductor version: Release (3.16)

sRACIPE 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.

Author: Vivek Kohar [aut, cre] , Mingyang Lu [aut]

Maintainer: Vivek Kohar <vivek.kohar at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sRACIPE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sRACIPE")

 

HTML	R Script	A systems biology tool for gene regulatory circuit simulation
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, GeneRegulation, GeneTarget, MathematicalBiology, ResearchField, Software, SystemsBiology
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0), SummarizedExperiment, methods, Rcpp
Imports	ggplot2, reshape2, MASS, RColorBrewer, gridExtra, visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics
LinkingTo	Rcpp
Suggests	knitr, BiocStyle, rmarkdown, tinytest, doFuture
SystemRequirements
Enhances
URL	https://vivekkohar.github.io/sRACIPE/ https://github.com/vivekkohar/sRACIPE https://geneex.jax.org/
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	sRACIPE_1.14.0.tar.gz
Windows Binary	sRACIPE_1.14.0.zip
macOS Binary (x86_64)	sRACIPE_1.14.0.tgz
macOS Binary (arm64)	sRACIPE_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sRACIPE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sRACIPE
Bioc Package Browser	https://code.bioconductor.org/browse/sRACIPE/
Package Short Url	https://bioconductor.org/packages/sRACIPE/
Package Downloads Report	Download Stats