Files in lusystemsbio/sRACIPE
Systems biology tool to simulate gene regulatory circuits
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
NEWS.md
R/AllClasses.R
R/AllGenerics.R
R/RcppExports.R
R/data.R
R/heatmapSimilarity.R
R/methods.R
R/sRACIPE.R
R/simulateGRC.R
R/utility.R
README.md
data/CoupledToggleSwitchSA.rda
data/EMT1.rda
data/EMT2.rda
data/cellCycle.rda
data/configData.rda
data/demoCircuit.rda
data/repressilator.rda
docs/404.html
docs/LICENSE-text.html
docs/articles/articles/simulatingTrajectories.html
docs/articles/articles/simulatingTrajectories_files/figure-html/unnamed-chunk-1-1.png
docs/articles/articles/simulatingTrajectories_files/figure-html/unnamed-chunk-2-1.png
docs/articles/articles/simulatingTrajectories_files/figure-html/unnamed-chunk-2-2.png
docs/articles/articles/simulatingTrajectories_files/figure-html/unnamed-chunk-4-1.png
docs/articles/articles/simulatingTrajectories_files/figure-html/unnamed-chunk-5-1.png
docs/articles/articles/singleModelSimulations.html
docs/articles/articles/singleModelSimulations_files/figure-html/unnamed-chunk-4-1.png
docs/articles/articles/singleModelSimulations_files/figure-html/unnamed-chunk-5-1.png
docs/articles/articles/underTheHood.html
docs/articles/index.html
docs/articles/sRACIPE.html
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-4-1.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-4-2.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-4-3.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-5-1.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-5-2.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-7-1.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-7-2.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-7-3.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-7-4.png
docs/articles/sRACIPE_files/figure-html/unnamed-chunk-7-5.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CoupledToggleSwitchSA.html
docs/reference/EMT1.html
docs/reference/EMT2.html
docs/reference/RacipeSE-class.html
docs/reference/RacipeSE.html
docs/reference/annotation-RacipeSE-method.html
docs/reference/annotation-set-RacipeSE-ANY-method.html
docs/reference/configData.html
docs/reference/demoCircuit.html
docs/reference/densityPlot.html
docs/reference/dot-ModelPvalue.html
docs/reference/dot-NthMin.html
docs/reference/dot-PermutedVar.html
docs/reference/dot-SimulatedPValueAbs.html
docs/reference/dot-SimulatedVarPValue.html
docs/reference/dot-loadNetworkFile.html
docs/reference/index.html
docs/reference/sRACIPE.html
docs/reference/sracipeCircuit-set.html
docs/reference/sracipeCircuit.html
docs/reference/sracipeConfig-set.html
docs/reference/sracipeConfig.html
docs/reference/sracipeGenParamNames.html
docs/reference/sracipeGetTS.html
docs/reference/sracipeHeatmapSimilarity.html
docs/reference/sracipeIC-set.html
docs/reference/sracipeIC.html
docs/reference/sracipeKnockDown.html
docs/reference/sracipeNormalize.html
docs/reference/sracipeOverExp.html
docs/reference/sracipeParams-set.html
docs/reference/sracipeParams.html
docs/reference/sracipePlotCircuit.html
docs/reference/sracipePlotData.html
docs/reference/sracipePlotParamBifur.html
docs/reference/sracipeSimulate.html
inputs/EMT_npjSystemsBiology.tpo
inputs/EMT_plosCompBio.tpo
inputs/FiveCoupledToggleSwitches.tpo
inputs/ToggleSwitch.tpo
inputs/ToggleSwitchOneActivation.tpo
inputs/ToggleSwitchTwoActivation.tpo
inputs/demoCircuit.txt
inputs/g2AB11.topo
inputs/sRACIPE.cfg
inputs/test.tpo
inst/CITATION
inst/logo/logo.png
inst/tinytest/testCircuit.R
inst/tinytest/tinytest.R
man/.Rapp.history
man/CoupledToggleSwitchSA.Rd
man/EMT1.Rd
man/EMT2.Rd
man/RacipeSE-class.Rd
man/RacipeSE.Rd
man/annotation-RacipeSE-method.Rd
man/annotation-set-RacipeSE-ANY-method.Rd
man/configData.Rd
man/demoCircuit.Rd
man/densityPlot.Rd
man/dot-ModelPvalue.Rd
man/dot-NthMin.Rd
man/dot-PermutedVar.Rd
man/dot-SimulatedPValueAbs.Rd
man/dot-SimulatedVarPValue.Rd
man/dot-loadNetworkFile.Rd
man/sRACIPE.Rd
man/sracipeCircuit-set.Rd
man/sracipeCircuit.Rd
man/sracipeCombineRacipeSE.Rd
man/sracipeConfig-set.Rd
man/sracipeConfig.Rd
man/sracipeConverge.Rd
man/sracipeConvergeDist.Rd
man/sracipeGenParamNames.Rd
man/sracipeGetTS.Rd
man/sracipeHeatmapSimilarity.Rd
man/sracipeIC-set.Rd
man/sracipeIC.Rd
man/sracipeKnockDown.Rd
man/sracipeNormalize.Rd
man/sracipeOverExp.Rd
man/sracipeParams-set.Rd
man/sracipeParams.Rd
man/sracipePlotCircuit.Rd
man/sracipePlotData.Rd
man/sracipePlotParamBifur.Rd
man/sracipeSimulate.Rd
man/sracipeUniqueStates.Rd
pkgdown/_pkgdown.yml
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
sRACIPE.Rproj
src/Makevars
src/RcppExports.cpp
src/generateThresholds.cpp
src/header.cpp
src/header.h
src/limitcycle.cpp
src/simulateGRC.cpp
src/steppers.cpp
src/steppersConv.cpp
vignettes/articles/heatmapSimilarity.Rmd
vignettes/articles/simulatingTrajectories.Rmd
vignettes/articles/singleModelSimulations.Rmd
vignettes/articles/underTheHood.Rmd
vignettes/sRACIPE.Rmd
www/racipe.png
