Package: ternarynet 1.49.0
McCall N. Matthew
ternarynet: Ternary Network Estimation
Gene-regulatory network (GRN) modeling seeks to infer dependencies between genes and thereby provide insight into the regulatory relationships that exist within a cell. This package provides a computational Bayesian approach to GRN estimation from perturbation experiments using a ternary network model, in which gene expression is discretized into one of 3 states: up, unchanged, or down). The ternarynet package includes a parallel implementation of the replica exchange Monte Carlo algorithm for fitting network models, using MPI.
Authors:
ternarynet_1.49.0.tar.gz
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ternarynet.pdf |ternarynet.html✨
ternarynet/json (API)
NEWS
| # Install 'ternarynet' in R: |
| install.packages('ternarynet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:ternarynet-1.49.0(bioc 3.20)ternarynet-1.48.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:4ec3c812e5
Exports:attractorSummarybackupStagebackupStage<-beta0beta0<-chi0chi0<-degreeObjMindegreeObjMin<-degreeObjsdegreeObjs<-deltadelta<-edgePenaltyedgePenalty<-epsilonepsilon<-experimentNamesexperimentNames<-finalTemperaturefinalTemperature<-geneNamesgeneNames<-graphObjMingraphObjMin<-graphObjsgraphObjs<-graphPosteriorinputParamsinputParams<-m0m0<-maxDegreemaxDegree<-maxStagemaxStage<-maxTransitionmaxTransition<-minScoreminScore<-nene<-neighborDegreeneighborDegree<-newScorenewScore<-pAddParentpAddParent<-parallelFitperturbationObjperturbationObj<-perturbationTypeperturbationType<-pExchangeParentpExchangeParent<-plotFitplotPostplotTracespNeighborhoodpNeighborhood<-predictAttractorrhorho<-scoresscores<-scoreTypescoreType<-simulateSteadyStatestageCountstageCount<-steadyStateObjsteadyStateObj<-tableObjMintableObjMin<-tableObjstableObjs<-ternaryFitternaryFitParametersternaryPosttnetfittnetposttracestraces<-xSeedxSeed<-
Dependencies:BHBiocParallelclicodetoolscpp11formatRfutile.loggerfutile.optionsglueigraphlambda.rlatticelifecyclemagrittrMatrixpkgconfigrlangsnowvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Summarize Attractors | attractorSummary |
| Network Topology | graphPosterior |
| Fit ternary network models using parallel tempering | parallelFit |
| Network Fit Plot | plotFit |
| Network Posterior Plot | plotPost |
| Network Fit Traces | plotTraces |
| Predict the attractor(s) resulting from a given perturbation | predictAttractor |
| Simulate Steady State Data | simulateSteadyState |
| Ternary Network Fit | class:ternaryFit degreeObjMin degreeObjMin,ternaryFit-method degreeObjMin<- degreeObjMin<-,ternaryFit-method dim,ternaryFit-method experimentNames experimentNames,ternaryFit-method experimentNames<- experimentNames<-,ternaryFit-method finalTemperature finalTemperature,ternaryFit-method finalTemperature<- finalTemperature<-,ternaryFit-method geneNames geneNames,ternaryFit-method geneNames<- geneNames<-,ternaryFit-method graphObjMin graphObjMin,ternaryFit-method graphObjMin<- graphObjMin<-,ternaryFit-method initialize,ternaryFit-method inputParams inputParams,ternaryFit-method inputParams<- inputParams<-,ternaryFit-method minScore minScore,ternaryFit-method minScore<- minScore<-,ternaryFit-method newScore newScore,ternaryFit-method newScore<- newScore<-,ternaryFit-method perturbationObj perturbationObj,ternaryFit-method perturbationObj<- perturbationObj<-,ternaryFit-method show,ternaryFit-method stageCount stageCount,ternaryFit-method stageCount<- stageCount<-,ternaryFit-method steadyStateObj steadyStateObj,ternaryFit-method steadyStateObj<- steadyStateObj<-,ternaryFit-method tableObjMin tableObjMin,ternaryFit-method tableObjMin<- tableObjMin<-,ternaryFit-method ternaryFit ternaryFit-class ternaryFit-methods traces traces,ternaryFit-method traces<- traces<-,ternaryFit-method xSeed xSeed,ternaryFit-method xSeed<- xSeed<-,ternaryFit-method |
| Ternary Network Fitting Parameters | backupStage backupStage,ternaryFitParameters-method backupStage<- backupStage<-,ternaryFitParameters-method beta0 beta0,ternaryFitParameters-method beta0<- beta0<-,ternaryFitParameters-method chi0 chi0,ternaryFitParameters-method chi0<- chi0<-,ternaryFitParameters-method class:ternaryFitParameters delta delta,ternaryFitParameters-method delta<- delta<-,ternaryFitParameters-method edgePenalty edgePenalty,ternaryFitParameters-method edgePenalty<- edgePenalty<-,ternaryFitParameters-method epsilon epsilon,ternaryFitParameters-method epsilon<- epsilon<-,ternaryFitParameters-method initialize,ternaryFitParameters-method m0 m0,ternaryFitParameters-method m0<- m0<-,ternaryFitParameters-method maxDegree maxDegree,ternaryFitParameters-method maxDegree<- maxDegree<-,ternaryFitParameters-method maxStage maxStage,ternaryFitParameters-method maxStage<- maxStage<-,ternaryFitParameters-method maxTransition maxTransition,ternaryFitParameters-method maxTransition<- maxTransition<-,ternaryFitParameters-method ne ne,ternaryFitParameters-method ne<- ne<-,ternaryFitParameters-method neighborDegree neighborDegree,ternaryFitParameters-method neighborDegree<- neighborDegree<-,ternaryFitParameters-method pAddParent pAddParent,ternaryFitParameters-method pAddParent<- pAddParent<-,ternaryFitParameters-method perturbationType perturbationType,ternaryFitParameters-method perturbationType<- perturbationType<-,ternaryFitParameters-method pExchangeParent pExchangeParent,ternaryFitParameters-method pExchangeParent<- pExchangeParent<-,ternaryFitParameters-method pNeighborhood pNeighborhood,ternaryFitParameters-method pNeighborhood<- pNeighborhood<-,ternaryFitParameters-method rho rho,ternaryFitParameters-method rho<- rho<-,ternaryFitParameters-method scoreType scoreType,ternaryFitParameters-method scoreType<- scoreType<-,ternaryFitParameters-method show,ternaryFitParameters-method ternaryFitParameters ternaryFitParameters-class ternaryFitParameters-methods |
| Ternary Network Posterior | class:ternaryPost degreeObjs degreeObjs,ternaryPost-method degreeObjs<- degreeObjs<-,ternaryPost-method dim,ternaryPost-method experimentNames,ternaryPost-method experimentNames<-,ternaryPost-method geneNames,ternaryPost-method geneNames<-,ternaryPost-method graphObjs graphObjs,ternaryPost-method graphObjs<- graphObjs<-,ternaryPost-method initialize,ternaryPost-method inputParams,ternaryPost-method inputParams<-,ternaryPost-method perturbationObj,ternaryPost-method perturbationObj<-,ternaryPost-method scores scores,ternaryPost-method scores<- scores<-,ternaryPost-method show,ternaryPost-method steadyStateObj,ternaryPost-method steadyStateObj<-,ternaryPost-method tableObjs tableObjs,ternaryPost-method tableObjs<- tableObjs<-,ternaryPost-method ternaryPost ternaryPost-class ternaryPost-methods |
| Ternary Network Fitting | tnetfit |
| Ternary Network Posterior Sampling | tnetpost |
