tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression
Version 1.30.0

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.

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AuthorAntti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence
Bioconductor views Bayesian GeneExpression GeneRegulation Microarray NetworkInference TimeCourse Transcription
Date of publicationNone
MaintainerAntti Honkela <antti.honkela@helsinki.fi>
LicenseAGPL-3
Version1.30.0
URL https://github.com/ahonkela/tigre
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("tigre")

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

CGoptim Man page Source code
ExpressionTimeSeries Man page
ExpressionTimeSeries-class Man page
GPLearn Man page Source code
GPModel Man page
GPModel-class Man page
GPPlot Man page Source code
GPRankTFs Man page Source code
GPRankTargets Man page Source code
SCGoptim Man page Source code
TF Man page
TF,scoreList-method Man page
TF<- Man page
TF<-,scoreList,character-method Man page
[,scoreList,ANY-method Man page
[,scoreList-method Man page
addAliases Source code
addAndGetAliasId Source code
addAndGetDatasetId Source code
addAndGetExperimentId Source code
addAndGetExperimentSetId Source code
addAndGetFigureId Source code
addAndGetProbeGeneIds Source code
addAndGetRegulatorId Source code
addAndGetSupplementaryDataId Source code
addExperimentSetExperiments Source code
addFigures Source code
addGeneAliases Source code
addResults Source code
addSupplementaryData Source code
addTargetSet Source code
addZscores Source code
baselineLogLikeGradient Source code
baselineLogLikelihood Source code
baselineOptimise Source code
baseloglikelihoods Man page
baseloglikelihoods,scoreList-method Man page
baseloglikelihoods<- Man page
baseloglikelihoods<-,scoreList,numeric-method Man page
boundedTransform Man page Source code
c,scoreList-method Man page
cgpdisimExpandParam Man page Source code
cgpdisimExtractParam Man page Source code
cgpdisimGradient Man page Source code
cgpdisimLogLikeGradients Man page Source code
cgpdisimLogLikelihood Man page Source code
cgpdisimObjective Man page Source code
cgpdisimUpdateProcesses Man page Source code
cgpsimExpandParam Man page Source code
cgpsimExtractParam Man page Source code
cgpsimGradient Man page Source code
cgpsimLogLikeGradients Man page Source code
cgpsimLogLikelihood Man page Source code
cgpsimObjective Man page Source code
cgpsimOptimise Man page Source code
cgpsimUpdateProcesses Man page Source code
cmpndKernCompute Man page Source code
cmpndKernDiagCompute Man page Source code
cmpndKernDiagGradX Man page Source code
cmpndKernDisplay Man page Source code
cmpndKernExpandParam Man page Source code
cmpndKernExtractParam Man page Source code
cmpndKernGradX Man page Source code
cmpndKernGradient Man page Source code
cmpndKernParamInit Man page Source code
complexLog Source code
createTables Source code
datasetName Man page
datasetName,scoreList-method Man page
datasetName<- Man page
datasetName<-,scoreList,character-method Man page
disimComputeH Source code
disimComputeHPrime Source code
disimKernCompute Man page Source code
disimKernDiagCompute Man page Source code
disimKernDisplay Man page Source code
disimKernExpandParam Man page Source code
disimKernExtractParam Man page Source code
disimKernGradient Man page Source code
disimKernParamInit Man page Source code
disimXdisimKernCompute Man page Source code
disimXdisimKernGradient Man page Source code
disimXrbfKernCompute Man page Source code
disimXrbfKernGradient Man page Source code
disimXsimKernCompute Man page Source code
disimXsimKernGradient Man page Source code
dist2 Source code
distfit Source code
distfit_obj Source code
drosophila_gpsim_fragment Man page
drosophila_mmgmos_fragment Man page
expTransform Man page Source code
experimentSet Man page
experimentSet,scoreList-method Man page
experimentSet<- Man page
experimentSet<-,scoreList,character-method Man page
export.scores Man page Source code
filterTargets Source code
fn_line Source code
formModel Source code
gammaPriorExpandParam Man page Source code
gammaPriorExtractParam Man page Source code
gammaPriorGradient Man page Source code
gammaPriorLogProb Man page Source code
gammaPriorParamInit Man page Source code
generateModels Man page Source code
genes Man page
genes,scoreList-method Man page
genes<- Man page
genes<-,scoreList,list-method Man page
getLoopVariables Source code
getProbeGeneId Source code
getProcessedData Source code
getVersion Source code
gpdisimCreate Man page Source code
gpdisimDisplay Man page Source code
gpdisimExpandParam Man page Source code
gpdisimExtractParam Man page Source code
gpdisimGradient Man page Source code
gpdisimLogLikeGradients Man page Source code
gpdisimLogLikelihood Man page Source code
gpdisimObjective Man page Source code
gpdisimUpdateProcesses Man page Source code
gpsimCreate Man page Source code
gpsimDisplay Man page Source code
gpsimExpandParam Man page Source code
gpsimExtractParam Man page Source code
gpsimGradient Man page Source code
gpsimKernelSpec Source code
gpsimLogLikeGradients Man page Source code
gpsimLogLikelihood Man page Source code
gpsimObjective Man page Source code
gpsimUpdateKernels Source code
gpsimUpdateProcesses Man page Source code
gradLnDiffErfs Source code
initialize,ExpressionTimeSeries-method Man page
initialize,GPModel-method Man page
invgammaPriorExpandParam Man page Source code
invgammaPriorExtractParam Man page Source code
invgammaPriorGradient Man page Source code
invgammaPriorLogProb Man page Source code
invgammaPriorParamInit Man page Source code
is.GPModel Man page Source code
is.GPModel,GPModel-method Man page
jitChol Source code
jitCholInv Source code
kernCompute Man page Source code
kernCreate Man page Source code
kernDiagCompute Man page Source code
kernDiagGradX Man page Source code
kernDisplay Man page Source code
kernExpandParam Man page Source code
kernExtractParam Man page Source code
kernFactors Source code
kernGradX Man page Source code
kernGradient Man page Source code
kernParamInit Man page Source code
kernPriorGradient Man page Source code
kernPriorLogProb Man page Source code
kernTestCombinationFunction Source code
knownTargets Man page
knownTargets,scoreList-method Man page
knownTargets<- Man page
knownTargets<-,scoreList,character-method Man page
length,scoreList-method Man page
listSelectSomeIndex Source code
lnDiffErfs Man page Source code
loglikelihoods Man page
loglikelihoods,scoreList-method Man page
loglikelihoods<- Man page
loglikelihoods<-,scoreList,numeric-method Man page
mlpKernCompute Man page Source code
mlpKernDiagGradX Man page Source code
mlpKernDiagGradXpoint Source code
mlpKernDisplay Man page
mlpKernExpandParam Man page Source code
mlpKernExtractParam Man page Source code
mlpKernGradX Man page Source code
mlpKernGradXpoint Source code
mlpKernGradient Man page Source code
mlpKernParamInit Man page Source code
modelArgs Man page
modelArgs,scoreList-method Man page
modelArgs<- Man page
modelArgs<-,scoreList,list-method Man page
modelDisplay Man page Source code
modelExpandParam Man page Source code
modelExtractParam Man page Source code
modelGradient Man page Source code
modelLogLikelihood Man page Source code
modelObjective Man page Source code
modelOptimise Man page Source code
modelStruct Man page
modelStruct,GPModel-method Man page
modelStruct<- Man page
modelStruct<-,GPModel,list-method Man page
modelTieParam Man page Source code
modelType Man page
modelType,GPModel-method Man page
modelUpdateProcesses Man page Source code
multiKernCacheBlock Source code
multiKernCompute Man page Source code
multiKernComputeBlock Source code
multiKernDiagCompute Man page Source code
multiKernDisplay Man page Source code
multiKernExpandParam Man page Source code
multiKernExtractParam Man page Source code
multiKernGradient Man page Source code
multiKernGradientBlock Source code
multiKernParamInit Man page Source code
openConnection Source code
optimiDefaultConstraint Man page Source code
optimiDefaultOptions Man page Source code
params Man page
params,scoreList-method Man page
params<- Man page
params<-,scoreList,list-method Man page
plotTimeseries Man page Source code
priorCreate Man page Source code
priorExpandParam Man page Source code
priorExtractParam Man page Source code
priorGradient Man page Source code
priorLogProb Man page Source code
priorParamInit Man page Source code
processData Man page Source code
processRawData Man page Source code
rbfKernCompute Man page Source code
rbfKernDiagCompute Man page Source code
rbfKernDisplay Man page Source code
rbfKernExpandParam Man page Source code
rbfKernExtractParam Man page Source code
rbfKernGradient Man page Source code
rbfKernParamInit Man page Source code
scoreList Man page
scoreList-class Man page
sharedModel Man page
sharedModel,scoreList-method Man page
sharedModel<- Man page
sharedModel<-,scoreList,list-method Man page
show,GPModel-method Man page
show,scoreList-method Man page
sigmoidTransform Man page Source code
simComputeH Source code
simKernCompute Man page Source code
simKernDiagCompute Man page Source code
simKernDisplay Man page Source code
simKernExpandParam Man page Source code
simKernExtractParam Man page Source code
simKernGradient Man page Source code
simKernParamInit Man page Source code
simXrbfKernCompute Man page Source code
simXrbfKernGradient Man page Source code
simXsimKernCompute Man page Source code
simXsimKernGradient Man page Source code
sort,scoreList-method Man page
tigre Man page
tigre-package Man page
translateKernCompute Man page Source code
translateKernDiagCompute Man page Source code
translateKernDisplay Man page
translateKernExpandParam Man page Source code
translateKernExtractParam Man page Source code
translateKernGradient Man page Source code
translateKernParamInit Man page Source code
var.exprs Man page
var.exprs,ExpressionTimeSeries-method Man page
var.exprs<- Man page
var.exprs<-,ExpressionTimeSeries-method Man page
whiteKernCompute Man page Source code
whiteKernDiagCompute Man page Source code
whiteKernDisplay Man page Source code
whiteKernExpandParam Man page Source code
whiteKernExtractParam Man page Source code
whiteKernGradient Man page Source code
whiteKernParamInit Man page Source code
whiteXwhiteKernCompute Man page Source code
whiteXwhiteKernGradient Man page Source code
write.scores Man page
write.scores,scoreList-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/GPPlot.R
R/GPrank.R
R/baselineFunctions.R
R/cmpndKernFunctions.R
R/disimKernFunctions.R
R/export.R
R/gammaPriorFunctions.R
R/gpdisimLinearFunctions.R
R/gpsimDatabase.R
R/gpsimLinearFunctions.R
R/invgammaPriorFunctions.R
R/kernFunctions.R
R/miscFunctions.R
R/mlpKernFunctions.R
R/optimiFunctions.R
R/priorFunctions.R
R/processData.R
R/rbfKernFunctions.R
R/simKernFunctions.R
R/translateKernFunctions.R
R/whiteKernFunctions.R
build
build/vignette.rds
data
data/drosophila_gpsim_fragment.RData
data/drosophila_mmgmos_fragment.RData
demos
demos/tp63.Rnw
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/tigre.R
inst/doc/tigre.Rnw
inst/doc/tigre.pdf
inst/doc/tigre_quick.R
inst/doc/tigre_quick.Rnw
inst/doc/tigre_quick.pdf
man
man/ExpressionTimeSeries-class.Rd
man/GPLearn.Rd
man/GPModel-class.Rd
man/GPPlot.Rd
man/GPRankTargets.Rd
man/SCGoptim.Rd
man/drosophila_gpsim_fragment.Rd
man/drosophila_mmgmos_fragment.Rd
man/expTransform.Rd
man/export.Rd
man/generateModels.Rd
man/gpsimCreate.Rd
man/kernCompute.Rd
man/kernCreate.Rd
man/kernDiagGradX.Rd
man/kernGradient.Rd
man/lnDiffErfs.Rd
man/modelDisplay.Rd
man/modelExpandParam.Rd
man/modelExtractParam.Rd
man/modelGradient.Rd
man/modelTieParam.Rd
man/optimiDefaultConstraint.Rd
man/plotTimeseries.Rd
man/processData.Rd
man/scoreList-class.Rd
man/tigre-package.Rd
src
src/miscCFunctions.c
vignettes
vignettes/build_vignette.sh
vignettes/gpsim.bib
vignettes/tigre-010.pdf
vignettes/tigre-011.pdf
vignettes/tigre-012.pdf
vignettes/tigre.Rnw
vignettes/tigre.Rnw.real_source
vignettes/tigre_quick.Rnw
tigre documentation built on May 20, 2017, 10:52 p.m.