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✨
card.svg |card.png
sRACIPE/json (API)
NEWS

# 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)

researchfieldsystemsbiologymathematicalbiologygeneexpressiongeneregulationgenetargetcpp

6.80 score 6 stars 234 scripts 356 downloads 1 mentions 27 exports 92 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksNOTE215
linux-devel-arm64NOTE271
linux-devel-x86_64NOTE320
source / vignettesOK311
linux-release-arm64NOTE267
linux-release-x86_64NOTE338
macos-release-arm64NOTE199
macos-release-x86_64NOTE408
macos-oldrel-arm64NOTE172
macos-oldrel-x86_64NOTE339
windows-develNOTE287
windows-releaseNOTE274
windows-oldrelNOTE237
wasm-releaseOK153

Exports:.RacipeSEannotationannotation<-densityPlotRacipeSEsracipeCircuitsracipeCircuit<-sracipeCombineRacipeSEsracipeConfigsracipeConfig<-sracipeConvergesracipeConvergeDistsracipeGenParamNamessracipeGetTSsracipeHeatmapSimilaritysracipeICsracipeIC<-sracipeKnockDownsracipeNormalizesracipeOverExpsracipeParamssracipeParams<-sracipePlotCircuitsracipePlotDatasracipePlotParamBifursracipeSimulatesracipeUniqueStates

Dependencies:abindaskpassbase64encBiobaseBiocGenericsbitopsbslibcachemcaToolsclicodetoolscpp11DelayedArraydigestdoFuturedoRNGevaluatefarverfastmapfontawesomeforeachfsfuturefuture.applygenericsGenomicRangesggplot2globalsgluegplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetsIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslparallellyplyrpngR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLreshape2reticulaterlangrmarkdownrngtoolsrprojrootRSpectraS4ArraysS4VectorsS7sassscalesSeqinfoSparseArraystringistringrSummarizedExperimentsystinytexumapvctrsviridisLitevisNetworkwithrxfunXVectoryaml

A systems biology tool for gene regulatory circuit simulation

Vivek Kohar, Aidan Tillman

Rendered fromsRACIPE.Rmdusingknitr::rmarkdownon May 30 2026.

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

Readme and manuals

Help Manual

Help pageTopics
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 simulationsallTypesDemoCircuit
A method to get the annotationannotation,RacipeSE-method
A method to set the circuit name or annotationannotation<-,RacipeSE,ANY-method
A circuit for modeling the yeast cell cyclecellCycle
Configuration DataconfigData
Five coupled toggle switchesCoupledToggleSwitchSA
A toggle switch circuit for demonstrationsdemoCircuit
Density PlotdensityPlot
A circuit for epithelial to mesenchymal transitionEMT1
A circuit for epithelial to mesenchymal transition including microRNAsEMT2
RacipeSE constructorRacipeSE
RacipeSE.RacipeSE RacipeSE-class
A loop motif for demonstrating limit cycles in gene expressionrepressilator
sRACIPE: A package for stochastic random circuit perturbation.sRACIPE-package sRACIPE
Method to get the circuitsracipeCircuit sracipeCircuit,RacipeSE-method
Initialize the circuitsracipeCircuit-set sracipeCircuit<- sracipeCircuit<-,RacipeSE-method
A method to combine RacipeSE objects with the same configsracipeCombineRacipeSE sracipeCombineRacipeSE,list-method
A method to access the simulation hyperparameterssracipeConfig sracipeConfig,RacipeSE-method
A method to access the simulation hyperparameterssracipeConfig-set sracipeConfig<- sracipeConfig<-,RacipeSE-method
A method to get the convergence results for deterministic simulationssracipeConverge sracipeConverge,RacipeSE-method
A method to visualize convergence distributionssracipeConvergeDist sracipeConvergeDist,RacipeSE-method
Generate parameter names for a circuitsracipeGenParamNames
A method to extract the time seriessracipeGetTS sracipeGetTS,RacipeSE-method
Calculates the similarity between two gene expression data.sracipeHeatmapSimilarity
A method to get the initial conditions used for simulationssracipeIC sracipeIC,RacipeSE-method
A method to set the initial conditionssracipeIC-set sracipeIC<- sracipeIC<-,RacipeSE-method
Perform in-silico knockdown analysissracipeKnockDown sracipeKnockDown,RacipeSE-method
Normalize the simulated gene expressionsracipeNormalize sracipeNormalize,RacipeSE-method
Perform in-silico over expression analysissracipeOverExp sracipeOverExp,RacipeSE-method
A method to access the simulation parameterssracipeParams sracipeParams,RacipeSE-method
A method to set the simulation parameterssracipeParams-set sracipeParams<- sracipeParams<-,RacipeSE-method
Plot Gene Regulatory CircuitsracipePlotCircuit sracipePlotCircuit,RacipeSE-method
Plot sRACIPE datasracipePlotData sracipePlotData,RacipeSE-method
Parameter bifurcation plotssracipePlotParamBifur sracipePlotParamBifur,RacipeSE-method
Simulate a gene regulatory circuitsracipeSimulate
A method for grabbing unique statessracipeUniqueStates sracipeUniqueStates,RacipeSE-method