sRACIPE
This is thereleased version of sRACIPE; for the devel version, seesRACIPE.
Systems biology tool to simulate gene regulatory circuits
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0001-8158-0593, Vivek Kohar [aut], Aidan Tillman [aut], Daniel Ramirez [aut]
Maintainer: Mingyang Lu <m.lu at northeastern.edu>
citation("sRACIPE")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("sRACIPE")For older versions of R, please refer to the appropriateBioconductor 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 | 2.2.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (6.5 years) |
| License | MIT + fileLICENSE |
| 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/sRACIPEhttps://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 |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | sRACIPE_2.2.0.tar.gz |
| Windows Binary (x86_64) | sRACIPE_2.2.0.zip |
| macOS Binary (x86_64) | sRACIPE_2.2.0.tgz |
| macOS Binary (arm64) | sRACIPE_2.2.0.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 |