tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression

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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.

Author
Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence
Date of publication
None
Maintainer
Antti Honkela <antti.honkela@hiit.fi>
License
AGPL-3
Version
1.28.0
URLs

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...

Files in this package

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