Package: sRACIPE 2.5.0

Mingyang Lu

sRACIPE: Systems biology tool to simulate gene regulatory circuits

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.

Authors:Mingyang Lu [aut, cre], Vivek Kohar [aut], Aidan Tillman [aut], Daniel Ramirez [aut]

sRACIPE_2.5.0.tar.gz
sRACIPE_2.5.0.zip(r-4.7)sRACIPE_2.5.0.zip(r-4.6)sRACIPE_2.5.0.zip(r-4.5)
sRACIPE_2.5.0.tgz(r-4.6-x86_64)sRACIPE_2.5.0.tgz(r-4.6-arm64)sRACIPE_2.5.0.tgz(r-4.5-x86_64)sRACIPE_2.5.0.tgz(r-4.5-arm64)
sRACIPE_2.5.0.tar.gz(r-4.7-arm64)sRACIPE_2.5.0.tar.gz(r-4.7-x86_64)sRACIPE_2.5.0.tar.gz(r-4.6-arm64)sRACIPE_2.5.0.tar.gz(r-4.6-x86_64)
sRACIPE_2.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sRACIPE/json (API)

# Install 'sRACIPE' in R:

install.packages('sRACIPE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lusystemsbio/sracipe/issues

Pkgdown/docs site:https://vivekkohar.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

allTypesDemoCircuit - A circuit with every interaction type for simulations
cellCycle - A circuit for modeling the yeast cell cycle
configData - Configuration Data
CoupledToggleSwitchSA - Five coupled toggle switches
demoCircuit - A toggle switch circuit for demonstrations
EMT1 - A circuit for epithelial to mesenchymal transition
EMT2 - A circuit for epithelial to mesenchymal transition including microRNAs
repressilator - A loop motif for demonstrating limit cycles in gene expression

On BioConductor:sRACIPE-2.5.0(bioc 3.24)sRACIPE-2.4.0(bioc 3.23)

researchfield systemsbiology mathematicalbiology geneexpression generegulation genetarget cpp

6.89 score 6 stars 287 scripts 1 mentions 27 exports 92 dependencies

Last updated from:b16c2dfb6b. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	238
linux-devel-arm64	NOTE	274
linux-devel-x86_64	NOTE	359
source / vignettes	OK	280
linux-release-arm64	NOTE	280
linux-release-x86_64	NOTE	355
macos-release-arm64	NOTE	201
macos-release-x86_64	NOTE	495
macos-oldrel-arm64	NOTE	228
macos-oldrel-x86_64	NOTE	334
windows-devel	NOTE	268
windows-release	NOTE	261
windows-oldrel	NOTE	245
wasm-release	OK	179

Exports:.RacipeSE annotation annotation<-densityPlot RacipeSE sracipeCircuit sracipeCircuit<-sracipeCombineRacipeSE sracipeConfig sracipeConfig<-sracipeConverge sracipeConvergeDist sracipeGenParamNames sracipeGetTS sracipeHeatmapSimilarity sracipeIC sracipeIC<-sracipeKnockDown sracipeNormalize sracipeOverExp sracipeParams sracipeParams<-sracipePlotCircuit sracipePlotData sracipePlotParamBifur sracipeSimulate sracipeUniqueStates

Dependencies:abind askpass base64enc Biobase BiocGenerics bitops bslib cachem caTools cli codetools cpp11 DelayedArray digest doFuture doRNG evaluate farver fastmap fontawesome foreach fs future future.apply generics GenomicRanges ggplot2 globals glue gplots gridExtra gtable gtools here highr htmltools htmlwidgets IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lattice lifecycle listenv magrittr MASS Matrix MatrixGenerics matrixStats memoise mime openssl parallelly plyr png R6 rappdirs RColorBrewer Rcpp RcppEigen RcppTOML reshape2 reticulate rlang rmarkdown rngtools rprojroot RSpectra S4Arrays S4Vectors S7 sass scales Seqinfo SparseArray stringi stringr SummarizedExperiment sys tinytex umap vctrs viridisLite visNetwork withr xfun XVector yaml

A systems biology tool for gene regulatory circuit simulation

Rendered fromsRACIPE.Rmdusingknitr::rmarkdown

Last update: 2025-02-25
Started: 2019-03-29

Help page	Topics
Loads the network/topology file.	.loadNetworkFile
Returns the variance array after permutations.	.ModelPvalue
Find nth minimum value from a vector	.NthMin
Find variance of permutations	.PermutedVar
Finds the variance corresponding to a given value.	.SimulatedPValueAbs
Finds the variance corresponding to a given value.	.SimulatedVarPValue
A circuit with every interaction type for simulations	allTypesDemoCircuit
A method to get the annotation	annotation,RacipeSE-method
A method to set the circuit name or annotation	annotation<-,RacipeSE,ANY-method
A circuit for modeling the yeast cell cycle	cellCycle
Configuration Data	configData
Five coupled toggle switches	CoupledToggleSwitchSA
A toggle switch circuit for demonstrations	demoCircuit
Density Plot	densityPlot
A circuit for epithelial to mesenchymal transition	EMT1
A circuit for epithelial to mesenchymal transition including microRNAs	EMT2
RacipeSE constructor	RacipeSE
RacipeSE	.RacipeSE RacipeSE-class
A loop motif for demonstrating limit cycles in gene expression	repressilator
sRACIPE: A package for stochastic random circuit perturbation.	sRACIPE-package sRACIPE
Method to get the circuit	sracipeCircuit sracipeCircuit,RacipeSE-method
Initialize the circuit	sracipeCircuit-set sracipeCircuit<- sracipeCircuit<-,RacipeSE-method
A method to combine RacipeSE objects with the same config	sracipeCombineRacipeSE sracipeCombineRacipeSE,list-method
A method to access the simulation hyperparameters	sracipeConfig sracipeConfig,RacipeSE-method
A method to access the simulation hyperparameters	sracipeConfig-set sracipeConfig<- sracipeConfig<-,RacipeSE-method
A method to get the convergence results for deterministic simulations	sracipeConverge sracipeConverge,RacipeSE-method
A method to visualize convergence distributions	sracipeConvergeDist sracipeConvergeDist,RacipeSE-method
Generate parameter names for a circuit	sracipeGenParamNames
A method to extract the time series	sracipeGetTS sracipeGetTS,RacipeSE-method
Calculates the similarity between two gene expression data.	sracipeHeatmapSimilarity
A method to get the initial conditions used for simulations	sracipeIC sracipeIC,RacipeSE-method
A method to set the initial conditions	sracipeIC-set sracipeIC<- sracipeIC<-,RacipeSE-method
Perform in-silico knockdown analysis	sracipeKnockDown sracipeKnockDown,RacipeSE-method
Normalize the simulated gene expression	sracipeNormalize sracipeNormalize,RacipeSE-method
Perform in-silico over expression analysis	sracipeOverExp sracipeOverExp,RacipeSE-method
A method to access the simulation parameters	sracipeParams sracipeParams,RacipeSE-method
A method to set the simulation parameters	sracipeParams-set sracipeParams<- sracipeParams<-,RacipeSE-method
Plot Gene Regulatory Circuit	sracipePlotCircuit sracipePlotCircuit,RacipeSE-method
Plot sRACIPE data	sracipePlotData sracipePlotData,RacipeSE-method
Parameter bifurcation plots	sracipePlotParamBifur sracipePlotParamBifur,RacipeSE-method
Simulate a gene regulatory circuit	sracipeSimulate
A method for grabbing unique states	sracipeUniqueStates sracipeUniqueStates,RacipeSE-method

Package: sRACIPE 2.5.0

sRACIPE: Systems biology tool to simulate gene regulatory circuits

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