Package: sRACIPE 1.99.1

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_1.99.1.tar.gz
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sRACIPE.pdf |sRACIPE.html✨
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 site:https://vivekkohar.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • CoupledToggleSwitchSA - Five coupled toggle switches
  • EMT1 - A circuit for epithelial to mesenchymal transition
  • EMT2 - A circuit for epithelial to mesenchymal transition including microRNAs
  • allTypesDemoCircuit - A circuit with every interaction type for simulations
  • cellCycle - A circuit for modeling the yeast cell cycle
  • configData - Configuration Data
  • demoCircuit - A toggle switch circuit for demonstrations
  • repressilator - A loop motif for demonstrating limit cycles in gene expression

On BioConductor:sRACIPE-1.99.1(bioc 3.21)sRACIPE-1.22.0(bioc 3.20)

researchfieldsystemsbiologymathematicalbiologygeneexpressiongeneregulationgenetargetcpp

6.40 score 4 stars 209 scripts 224 downloads 1 mentions 27 exports 104 dependencies

Last updated 30 days agofrom:bce5d5dcfc. Checks:1 OK, 11 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 27 2025
R-4.5-win-x86_64NOTEMar 27 2025
R-4.5-mac-x86_64NOTEMar 27 2025
R-4.5-mac-aarch64NOTEMar 27 2025
R-4.5-linux-x86_64NOTEMar 27 2025
R-4.4-win-x86_64NOTEMar 27 2025
R-4.4-mac-x86_64NOTEMar 27 2025
R-4.4-mac-aarch64NOTEMar 27 2025
R-4.4-linux-x86_64NOTEMar 27 2025
R-4.3-win-x86_64NOTEMar 27 2025
R-4.3-mac-x86_64NOTEMar 27 2025
R-4.3-mac-aarch64NOTEMar 27 2025

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

Dependencies:abindaskpassbase64encBiobaseBiocGenericsbitopsbslibcachemcaToolsclicodetoolscolorspacecrayoncurlDelayedArraydigestdoFuturedoRNGevaluatefansifarverfastmapfontawesomeforeachfsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsgluegplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslparallellypillarpkgconfigplyrpngR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLreshape2reticulaterlangrmarkdownrngtoolsrprojrootRSpectraS4ArraysS4VectorssassscalesSparseArraystringistringrSummarizedExperimentsystibbletinytexUCSC.utilsumaputf8vctrsviridisLitevisNetworkwithrxfunXVectoryaml

A systems biology tool for gene regulatory circuit simulation

Vivek Kohar, Aidan Tillman

Rendered fromsRACIPE.Rmdusingknitr::rmarkdownon Mar 27 2025.

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