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 (3.24)
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: Mingyang Lu [aut, cre] 
, Vivek Kohar [aut], Aidan Tillman [aut], Daniel Ramirez [aut]
Maintainer: Mingyang Lu <m.lu at northeastern.edu>
citation("sRACIPE")):Mingyang Lu, Vivek Kohar, Aidan Tillman, Daniel Ramirez. sRACIPE: Systems biology tool to simulate gene regulatory circuits. doi:10.18129/B9.bioc.sRACIPE, R package version 2.5.0, https://bioconductor.org/packages/sRACIPE.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneRegulation, GeneTarget, MathematicalBiology, ResearchField, Software, SystemsBiology |
| Version | 2.5.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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, doFuture, doRNG, future, foreach |
| System Requirements | |
| URL | https://github.com/lusystemsbio/sRACIPE https://geneex.jax.org/ https://vivekkohar.github.io/sRACIPE/ |
See More
| Suggests | knitr, BiocStyle, rmarkdown, tinytest |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sRACIPE_2.5.0.tar.gz |
| Windows Binary (x86_64) | sRACIPE_2.5.0.zip |
| macOS Binary (big-sur-x86_64) | sRACIPE_2.5.0.tgz |
| macOS Binary (sonoma-arm64) | sRACIPE_2.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sRACIPE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sRACIPE |
| Package Short Url | https://bioconductor.org/packages/sRACIPE/ |
| Package Downloads Report | Download Stats |