Package: tigre 1.59.0
Antti Honkela
tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression
The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.
Authors:
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tigre.pdf |tigre.html✨
tigre/json (API)
NEWS
| # Install 'tigre' in R: |
| install.packages('tigre', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ahonkela/tigre/issues
- drosophila_gpsim_fragment - Fragment of 12 time point Drosophila embryonic development microarray gene expression time series
- drosophila_mmgmos_fragment - Fragment of 12 time point Drosophila embryonic development microarray gene expression time series
On BioConductor:tigre-1.59.0(bioc 3.20)tigre-1.58.0(bioc 3.19)
Last updated 2 months agofrom:59d8655c9f
Exports:baseloglikelihoodsbaseloglikelihoods<-boundedTransformCGoptimcgpdisimExpandParamcgpdisimExtractParamcgpdisimGradientcgpdisimLogLikeGradientscgpdisimLogLikelihoodcgpdisimObjectivecgpdisimUpdateProcessescgpsimExpandParamcgpsimExtractParamcgpsimGradientcgpsimLogLikeGradientscgpsimLogLikelihoodcgpsimObjectivecgpsimOptimisecgpsimUpdateProcessescmpndKernComputecmpndKernDiagComputecmpndKernDiagGradXcmpndKernDisplaycmpndKernExpandParamcmpndKernExtractParamcmpndKernGradientcmpndKernGradXcmpndKernParamInitdatasetNamedatasetName<-disimKernComputedisimKernDiagComputedisimKernDisplaydisimKernExpandParamdisimKernExtractParamdisimKernGradientdisimKernParamInitdisimXdisimKernComputedisimXdisimKernGradientdisimXrbfKernComputedisimXrbfKernGradientdisimXsimKernComputedisimXsimKernGradientexperimentSetexperimentSet<-export.scoresexpTransformgammaPriorExpandParamgammaPriorExtractParamgammaPriorGradientgammaPriorLogProbgammaPriorParamInitgenerateModelsgenesgenes<-gpdisimCreategpdisimDisplaygpdisimExpandParamgpdisimExtractParamgpdisimGradientgpdisimLogLikeGradientsgpdisimLogLikelihoodgpdisimObjectivegpdisimUpdateProcessesGPLearnGPPlotGPRankTargetsGPRankTFsgpsimCreategpsimDisplaygpsimExpandParamgpsimExtractParamgpsimGradientgpsimLogLikeGradientsgpsimLogLikelihoodgpsimObjectivegpsimUpdateProcessesinvgammaPriorExpandParaminvgammaPriorExtractParaminvgammaPriorGradientinvgammaPriorLogProbinvgammaPriorParamInitis.GPModelkernComputekernCreatekernDiagComputekernDiagGradXkernDisplaykernExpandParamkernExtractParamkernGradientkernGradXkernParamInitkernPriorGradientkernPriorLogProbknownTargetsknownTargets<-lnDiffErfsloglikelihoodsloglikelihoods<-mlpKernComputemlpKernDiagGradXmlpKernExpandParammlpKernExtractParammlpKernGradientmlpKernGradXmlpKernParamInitmodelArgsmodelArgs<-modelDisplaymodelExpandParammodelExtractParammodelGradientmodelLogLikelihoodmodelObjectivemodelOptimisemodelStructmodelStruct<-modelTieParammodelTypemodelUpdateProcessesmultiKernComputemultiKernDiagComputemultiKernDisplaymultiKernExpandParammultiKernExtractParammultiKernGradientmultiKernParamInitoptimiDefaultConstraintoptimiDefaultOptionsparamsparams<-plotTimeseriespriorCreatepriorExpandParampriorExtractParampriorGradientpriorLogProbpriorParamInitprocessDataprocessRawDatarbfKernComputerbfKernDiagComputerbfKernDisplayrbfKernExpandParamrbfKernExtractParamrbfKernGradientrbfKernParamInitSCGoptimsharedModelsharedModel<-sigmoidTransformsimKernComputesimKernDiagComputesimKernDisplaysimKernExpandParamsimKernExtractParamsimKernGradientsimKernParamInitsimXrbfKernComputesimXrbfKernGradientsimXsimKernComputesimXsimKernGradientTFTF<-translateKernComputetranslateKernDiagComputetranslateKernExpandParamtranslateKernExtractParamtranslateKernGradienttranslateKernParamInitvar.exprsvar.exprs<-whiteKernComputewhiteKernDiagComputewhiteKernDisplaywhiteKernExpandParamwhiteKernExtractParamwhiteKernGradientwhiteKernParamInitwhiteXwhiteKernComputewhiteXwhiteKernGradientwrite.scores
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemcaToolsclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDatagluegplotsgtoolshttrIRangesjsonliteKEGGRESTKernSmoothlifecyclememoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorssysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| tigre - Transcription factor Inference through Gaussian process Reconstruction of Expression | tigre-package tigre |
| Fragment of 12 time point Drosophila embryonic development microarray gene expression time series | drosophila_gpsim_fragment |
| Fragment of 12 time point Drosophila embryonic development microarray gene expression time series | drosophila_mmgmos_fragment |
| Export results to an SQLite database | export.scores |
| Class to contain time series expression assays | ExpressionTimeSeries ExpressionTimeSeries-class initialize,ExpressionTimeSeries-method var.exprs var.exprs,ExpressionTimeSeries-method var.exprs<- var.exprs<-,ExpressionTimeSeries-method |
| Constrains a parameter. | boundedTransform expTransform sigmoidTransform |
| Generating models with the given data | generateModels |
| Fit a GP model | GPLearn |
| A container for gpsim models | GPModel GPModel-class initialize,GPModel-method is.GPModel is.GPModel,GPModel-method modelStruct modelStruct,GPModel-method modelStruct<- modelStruct<-,GPModel,list-method modelType modelType,GPModel-method show,GPModel-method |
| Plot GP(DI)SIM models | GPPlot |
| Ranking possible target genes or regulators | GPRankTargets GPRankTFs |
| Create a GPSIM/GPDISIM model. | gpdisimCreate gpsimCreate |
| Compute the kernel given the parameters and X. | cmpndKernCompute cmpndKernDiagCompute disimKernCompute disimKernDiagCompute disimXdisimKernCompute disimXrbfKernCompute disimXsimKernCompute kernCompute kernDiagCompute mlpKernCompute multiKernCompute multiKernDiagCompute rbfKernCompute rbfKernDiagCompute simKernCompute simKernDiagCompute simXrbfKernCompute simXsimKernCompute translateKernCompute translateKernDiagCompute whiteKernCompute whiteKernDiagCompute whiteXwhiteKernCompute |
| Initialise a kernel structure. | cmpndKernParamInit disimKernParamInit gammaPriorParamInit invgammaPriorParamInit kernCreate kernParamInit mlpKernParamInit multiKernParamInit priorCreate priorParamInit rbfKernParamInit simKernParamInit translateKernParamInit whiteKernParamInit |
| Compute the gradient of the kernel wrt X. | cmpndKernDiagGradX cmpndKernGradX kernDiagGradX kernGradX mlpKernDiagGradX mlpKernGradX |
| Compute the gradient wrt the kernel parameters. | cmpndKernGradient disimKernGradient disimXdisimKernGradient disimXrbfKernGradient disimXsimKernGradient kernGradient mlpKernGradient multiKernGradient rbfKernGradient simKernGradient simXrbfKernGradient simXsimKernGradient translateKernGradient whiteKernGradient whiteXwhiteKernGradient |
| Helper function for computing the log of difference | lnDiffErfs |
| Display a model. | cmpndKernDisplay disimKernDisplay gpdisimDisplay gpsimDisplay kernDisplay modelDisplay multiKernDisplay rbfKernDisplay simKernDisplay whiteKernDisplay |
| Update a model structure with new parameters or update the posterior processes. | cgpdisimExpandParam cgpdisimUpdateProcesses cgpsimExpandParam cgpsimUpdateProcesses cmpndKernExpandParam disimKernExpandParam gammaPriorExpandParam gpdisimExpandParam gpdisimUpdateProcesses gpsimExpandParam gpsimUpdateProcesses invgammaPriorExpandParam kernExpandParam mlpKernExpandParam modelExpandParam modelUpdateProcesses multiKernExpandParam priorExpandParam rbfKernExpandParam simKernExpandParam translateKernExpandParam whiteKernExpandParam |
| Extract the parameters of a model. | cgpdisimExtractParam cgpsimExtractParam cmpndKernExtractParam disimKernExtractParam gammaPriorExtractParam gpdisimExtractParam gpsimExtractParam invgammaPriorExtractParam kernExtractParam mlpKernExtractParam modelExtractParam multiKernExtractParam priorExtractParam rbfKernExtractParam simKernExtractParam translateKernExtractParam whiteKernExtractParam |
| Model log-likelihood/objective error function and its gradient. | cgpdisimGradient cgpdisimLogLikeGradients cgpdisimLogLikelihood cgpdisimObjective cgpsimGradient cgpsimLogLikeGradients cgpsimLogLikelihood cgpsimObjective gammaPriorGradient gammaPriorLogProb gpdisimGradient gpdisimLogLikeGradients gpdisimLogLikelihood gpdisimObjective gpsimGradient gpsimLogLikeGradients gpsimLogLikelihood gpsimObjective invgammaPriorGradient invgammaPriorLogProb kernPriorGradient kernPriorLogProb modelGradient modelLogLikelihood modelObjective priorGradient priorLogProb |
| Tie parameters of a model together. | modelTieParam |
| Returns function for parameter constraint. | optimiDefaultConstraint |
| Plot ExpressionTimeSeries data | plotTimeseries |
| Processing expression time series | processData processRawData |
| Optimise the given function using (scaled) conjugate gradients. | CGoptim cgpsimOptimise modelOptimise optimiDefaultOptions SCGoptim |
| Class "scoreList" | baseloglikelihoods baseloglikelihoods,scoreList-method baseloglikelihoods<- baseloglikelihoods<-,scoreList,numeric-method c,scoreList-method datasetName datasetName,scoreList-method datasetName<- datasetName<-,scoreList,character-method experimentSet experimentSet,scoreList-method experimentSet<- experimentSet<-,scoreList,character-method genes genes,scoreList-method genes<- genes<-,scoreList,list-method knownTargets knownTargets,scoreList-method knownTargets<- knownTargets<-,scoreList,character-method length,scoreList-method loglikelihoods loglikelihoods,scoreList-method loglikelihoods<- loglikelihoods<-,scoreList,numeric-method modelArgs modelArgs,scoreList-method modelArgs<- modelArgs<-,scoreList,list-method params params,scoreList-method params<- params<-,scoreList,list-method scoreList scoreList-class sharedModel sharedModel,scoreList-method sharedModel<- sharedModel<-,scoreList,list-method show,scoreList-method sort,scoreList-method TF TF,scoreList-method TF<- TF<-,scoreList,character-method write.scores write.scores,scoreList-method [,scoreList,ANY-method [,scoreList-method |
