GRENITS: Gene Regulatory Network Inference Using Time Series

The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GRENITS")
AuthorEdward Morrissey
Bioconductor views Bayesian GeneExpression GeneRegulation GraphAndNetwork Network NetworkInference TimeCourse
Date of publicationNone
MaintainerEdward Morrissey <edward.morrissey@gmail.com>
LicenseGPL (>= 2)
Version1.28.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/AR1_Error_functions.R R/AR1_Error_functions_student.R R/AR1_functions.R R/AnalyseOutput_MCMC.R R/Splines_functions.R R/convergenceAR1.R R/convergenceReps_gauss.R R/convergenceReps_student.R R/convergenceSplines.R R/defaultMCMC_params.R R/genericAnalysisFunctions.R R/plotPriors.R R/readChains.R
build
build/vignette.rds
data
data/Athaliana_ODE.txt
data/Athaliana_ODE_4NoiseReps.txt
inst
inst/NEWS
inst/doc
inst/doc/GRENITS_package.R
inst/doc/GRENITS_package.Rnw
inst/doc/GRENITS_package.pdf
man
man/LockeData.Rd man/LockeDataError.Rd man/analyse.output.Rd man/defaultParams_gauss.Rd man/defaultParams_linear.Rd man/defaultParams_nonLinear.Rd man/defaultParams_student.Rd man/function_LinearNet.Rd man/function_NonLinearNet.Rd man/function_ReplicatesNet_gauss.Rd man/function_ReplicatesNet_student.Rd man/plotPriors.Rd man/readChains.Rd
src
src/AR1_Gauss_biocond.cc
src/AR1_Gauss_biocond.h
src/AR1_Student_biocond.cc
src/AR1_Student_biocond.h
src/AR1_biocond.cc
src/AR1_biocond.h
src/Makevars
src/Makevars.win
src/PSplines_biocond.cc
src/PSplines_biocond.h
src/R_C_interface.cpp
src/ReadMCMCFiles.cpp
src/ReadMCMCFiles.h
src/commonFunctions.cc
src/commonFunctions.h
src/functionsErrorModel.cc
src/functionsErrorModel.h
src/matrixManipulationFunctions.cc
src/matrixManipulationFunctions.h
src/updateFunctions_AR1.cc
src/updateFunctions_AR1.h
src/updateFunctions_Splines.cc
src/updateFunctions_Splines.h
vignettes
vignettes/GRENITS_package.Rnw

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