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.

AuthorAntti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence
Date of publicationNone
MaintainerAntti Honkela <antti.honkela@hiit.fi>
LicenseAGPL-3
Version1.28.0
https://github.com/ahonkela/tigre

View on Bioconductor

Man pages

drosophila_gpsim_fragment: Fragment of 12 time point Drosophila embryonic development...

drosophila_mmgmos_fragment: Fragment of 12 time point Drosophila embryonic development...

export: Export results to an SQLite database

ExpressionTimeSeries-class: Class to contain time series expression assays

expTransform: Constrains a parameter.

generateModels: Generating models with the given data

GPLearn: Fit a GP model

GPModel-class: A container for gpsim models

GPPlot: Plot GP(DI)SIM models

GPRankTargets: Ranking possible target genes or regulators

gpsimCreate: Create a GPSIM/GPDISIM model.

kernCompute: Compute the kernel given the parameters and X.

kernCreate: Initialise a kernel structure.

kernDiagGradX: Compute the gradient of the kernel wrt X.

kernGradient: Compute the gradient wrt the kernel parameters.

lnDiffErfs: Helper function for computing the log of difference

modelDisplay: Display a model.

modelExpandParam: Update a model structure with new parameters or update the...

modelExtractParam: Extract the parameters of a model.

modelGradient: Model log-likelihood/objective error function and its...

modelTieParam: Tie parameters of a model together.

optimiDefaultConstraint: Returns function for parameter constraint.

plotTimeseries: Plot ExpressionTimeSeries data

processData: Processing expression time series

SCGoptim: Optimise the given function using (scaled) conjugate...

scoreList-class: Class "scoreList"

tigre-package: tigre - Transcription factor Inference through Gaussian...

Functions

baseloglikelihoods Man page
baseloglikelihoods<- Man page
baseloglikelihoods,scoreList-method Man page
baseloglikelihoods<-,scoreList,numeric-method Man page
boundedTransform Man page
CGoptim Man page
cgpdisimExpandParam Man page
cgpdisimExtractParam Man page
cgpdisimGradient Man page
cgpdisimLogLikeGradients Man page
cgpdisimLogLikelihood Man page
cgpdisimObjective Man page
cgpdisimUpdateProcesses Man page
cgpsimExpandParam Man page
cgpsimExtractParam Man page
cgpsimGradient Man page
cgpsimLogLikeGradients Man page
cgpsimLogLikelihood Man page
cgpsimObjective Man page
cgpsimOptimise Man page
cgpsimUpdateProcesses Man page
cmpndKernCompute Man page
cmpndKernDiagCompute Man page
cmpndKernDiagGradX Man page
cmpndKernDisplay Man page
cmpndKernExpandParam Man page
cmpndKernExtractParam Man page
cmpndKernGradient Man page
cmpndKernGradX Man page
cmpndKernParamInit Man page
c,scoreList-method Man page
datasetName Man page
datasetName<- Man page
datasetName<-,scoreList,character-method Man page
datasetName,scoreList-method Man page
disimKernCompute Man page
disimKernDiagCompute Man page
disimKernDisplay Man page
disimKernExpandParam Man page
disimKernExtractParam Man page
disimKernGradient Man page
disimKernParamInit Man page
disimXdisimKernCompute Man page
disimXdisimKernGradient Man page
disimXrbfKernCompute Man page
disimXrbfKernGradient Man page
disimXsimKernCompute Man page
disimXsimKernGradient Man page
drosophila_gpsim_fragment Man page
drosophila_mmgmos_fragment Man page
experimentSet Man page
experimentSet<- Man page
experimentSet<-,scoreList,character-method Man page
experimentSet,scoreList-method Man page
export.scores Man page
ExpressionTimeSeries Man page
ExpressionTimeSeries-class Man page
expTransform Man page
gammaPriorExpandParam Man page
gammaPriorExtractParam Man page
gammaPriorGradient Man page
gammaPriorLogProb Man page
gammaPriorParamInit Man page
generateModels Man page
genes Man page
genes<- Man page
genes<-,scoreList,list-method Man page
genes,scoreList-method Man page
gpdisimCreate Man page
gpdisimDisplay Man page
gpdisimExpandParam Man page
gpdisimExtractParam Man page
gpdisimGradient Man page
gpdisimLogLikeGradients Man page
gpdisimLogLikelihood Man page
gpdisimObjective Man page
gpdisimUpdateProcesses Man page
GPLearn Man page
GPModel Man page
GPModel-class Man page
GPPlot Man page
GPRankTargets Man page
GPRankTFs Man page
gpsimCreate Man page
gpsimDisplay Man page
gpsimExpandParam Man page
gpsimExtractParam Man page
gpsimGradient Man page
gpsimLogLikeGradients Man page
gpsimLogLikelihood Man page
gpsimObjective Man page
gpsimUpdateProcesses Man page
initialize,ExpressionTimeSeries-method Man page
initialize,GPModel-method Man page
invgammaPriorExpandParam Man page
invgammaPriorExtractParam Man page
invgammaPriorGradient Man page
invgammaPriorLogProb Man page
invgammaPriorParamInit Man page
is.GPModel Man page
is.GPModel,GPModel-method Man page
kernCompute Man page
kernCreate Man page
kernDiagCompute Man page
kernDiagGradX Man page
kernDisplay Man page
kernExpandParam Man page
kernExtractParam Man page
kernGradient Man page
kernGradX Man page
kernParamInit Man page
kernPriorGradient Man page
kernPriorLogProb Man page
knownTargets Man page
knownTargets<- Man page
knownTargets<-,scoreList,character-method Man page
knownTargets,scoreList-method Man page
length,scoreList-method Man page
lnDiffErfs Man page
loglikelihoods Man page
loglikelihoods<- Man page
loglikelihoods,scoreList-method Man page
loglikelihoods<-,scoreList,numeric-method Man page
mlpKernCompute Man page
mlpKernDiagGradX Man page
mlpKernDisplay Man page
mlpKernExpandParam Man page
mlpKernExtractParam Man page
mlpKernGradient Man page
mlpKernGradX Man page
mlpKernParamInit Man page
modelArgs Man page
modelArgs<- Man page
modelArgs<-,scoreList,list-method Man page
modelArgs,scoreList-method Man page
modelDisplay Man page
modelExpandParam Man page
modelExtractParam Man page
modelGradient Man page
modelLogLikelihood Man page
modelObjective Man page
modelOptimise Man page
modelStruct Man page
modelStruct<- Man page
modelStruct<-,GPModel,list-method Man page
modelStruct,GPModel-method Man page
modelTieParam Man page
modelType Man page
modelType,GPModel-method Man page
modelUpdateProcesses Man page
multiKernCompute Man page
multiKernDiagCompute Man page
multiKernDisplay Man page
multiKernExpandParam Man page
multiKernExtractParam Man page
multiKernGradient Man page
multiKernParamInit Man page
optimiDefaultConstraint Man page
optimiDefaultOptions Man page
params Man page
params<- Man page
params<-,scoreList,list-method Man page
params,scoreList-method Man page
plotTimeseries Man page
priorCreate Man page
priorExpandParam Man page
priorExtractParam Man page
priorGradient Man page
priorLogProb Man page
priorParamInit Man page
processData Man page
processRawData Man page
rbfKernCompute Man page
rbfKernDiagCompute Man page
rbfKernDisplay Man page
rbfKernExpandParam Man page
rbfKernExtractParam Man page
rbfKernGradient Man page
rbfKernParamInit Man page
SCGoptim Man page
scoreList Man page
[,scoreList,ANY-method Man page
scoreList-class Man page
[,scoreList-method Man page
sharedModel Man page
sharedModel<- Man page
sharedModel<-,scoreList,list-method Man page
sharedModel,scoreList-method Man page
show,GPModel-method Man page
show,scoreList-method Man page
sigmoidTransform Man page
simKernCompute Man page
simKernDiagCompute Man page
simKernDisplay Man page
simKernExpandParam Man page
simKernExtractParam Man page
simKernGradient Man page
simKernParamInit Man page
simXrbfKernCompute Man page
simXrbfKernGradient Man page
simXsimKernCompute Man page
simXsimKernGradient Man page
sort,scoreList-method Man page
TF Man page
TF<- Man page
TF<-,scoreList,character-method Man page
TF,scoreList-method Man page
tigre Man page
tigre-package Man page
translateKernCompute Man page
translateKernDiagCompute Man page
translateKernDisplay Man page
translateKernExpandParam Man page
translateKernExtractParam Man page
translateKernGradient Man page
translateKernParamInit Man page
var.exprs Man page
var.exprs<- Man page
var.exprs<-,ExpressionTimeSeries-method Man page
var.exprs,ExpressionTimeSeries-method Man page
whiteKernCompute Man page
whiteKernDiagCompute Man page
whiteKernDisplay Man page
whiteKernExpandParam Man page
whiteKernExtractParam Man page
whiteKernGradient Man page
whiteKernParamInit Man page
whiteXwhiteKernCompute Man page
whiteXwhiteKernGradient Man page
write.scores Man page
write.scores,scoreList-method Man page

Files

tigre/DESCRIPTION
tigre/NAMESPACE
tigre/R
tigre/R/AllClasses.R tigre/R/GPPlot.R tigre/R/GPrank.R tigre/R/baselineFunctions.R tigre/R/cmpndKernFunctions.R tigre/R/disimKernFunctions.R tigre/R/export.R tigre/R/gammaPriorFunctions.R tigre/R/gpdisimLinearFunctions.R tigre/R/gpsimDatabase.R tigre/R/gpsimLinearFunctions.R tigre/R/invgammaPriorFunctions.R tigre/R/kernFunctions.R tigre/R/miscFunctions.R tigre/R/mlpKernFunctions.R tigre/R/optimiFunctions.R tigre/R/priorFunctions.R tigre/R/processData.R tigre/R/rbfKernFunctions.R tigre/R/simKernFunctions.R tigre/R/translateKernFunctions.R tigre/R/whiteKernFunctions.R
tigre/build
tigre/build/vignette.rds
tigre/data
tigre/data/drosophila_gpsim_fragment.RData
tigre/data/drosophila_mmgmos_fragment.RData
tigre/demos
tigre/demos/tp63.Rnw
tigre/inst
tigre/inst/CITATION
tigre/inst/NEWS
tigre/inst/doc
tigre/inst/doc/tigre.R
tigre/inst/doc/tigre.Rnw
tigre/inst/doc/tigre.pdf
tigre/inst/doc/tigre_quick.R
tigre/inst/doc/tigre_quick.Rnw
tigre/inst/doc/tigre_quick.pdf
tigre/man
tigre/man/ExpressionTimeSeries-class.Rd tigre/man/GPLearn.Rd tigre/man/GPModel-class.Rd tigre/man/GPPlot.Rd tigre/man/GPRankTargets.Rd tigre/man/SCGoptim.Rd tigre/man/drosophila_gpsim_fragment.Rd tigre/man/drosophila_mmgmos_fragment.Rd tigre/man/expTransform.Rd tigre/man/export.Rd tigre/man/generateModels.Rd tigre/man/gpsimCreate.Rd tigre/man/kernCompute.Rd tigre/man/kernCreate.Rd tigre/man/kernDiagGradX.Rd tigre/man/kernGradient.Rd tigre/man/lnDiffErfs.Rd tigre/man/modelDisplay.Rd tigre/man/modelExpandParam.Rd tigre/man/modelExtractParam.Rd tigre/man/modelGradient.Rd tigre/man/modelTieParam.Rd tigre/man/optimiDefaultConstraint.Rd tigre/man/plotTimeseries.Rd tigre/man/processData.Rd tigre/man/scoreList-class.Rd tigre/man/tigre-package.Rd
tigre/src
tigre/src/miscCFunctions.c
tigre/vignettes
tigre/vignettes/build_vignette.sh
tigre/vignettes/gpsim.bib
tigre/vignettes/tigre-010.pdf
tigre/vignettes/tigre-011.pdf
tigre/vignettes/tigre-012.pdf
tigre/vignettes/tigre.Rnw
tigre/vignettes/tigre.Rnw.real_source
tigre/vignettes/tigre_quick.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.