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sRACIPE

This is the development version of sRACIPE; for the stable release version, see sRACIPE.

Systems biology tool to simulate gene regulatory circuits


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("sRACIPE")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneExpression, GeneRegulation, GeneTarget, MathematicalBiology, ResearchField, Software, SystemsBiology
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 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
System Requirements
URL https://vivekkohar.github.io/sRACIPE/ https://github.com/vivekkohar/sRACIPE https://geneex.jax.org/
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Suggests knitr, BiocStyle, rmarkdown, tinytest, doFuture
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package sRACIPE_1.19.0.tar.gz
Windows Binary sRACIPE_1.19.0.zip
macOS Binary (x86_64) sRACIPE_1.19.0.tgz
macOS Binary (arm64) sRACIPE_1.19.0.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