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...

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

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