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.

Author
Edward Morrissey
Date of publication
None
Maintainer
Edward Morrissey <edward.morrissey@gmail.com>
License
GPL (>= 2)
Version
1.26.0

View on Bioconductor

Man pages

analyse.output
Analysis Plots
defaultParams_gauss
Default Parameters for Linear Model with Gaussian distributed...
defaultParams_linear
Default Parameters for Linear Model
defaultParams_nonLinear
Default Parameters for non-Linear Model
defaultParams_student
Default Parameters for Linear Model with Student distributed...
function_LinearNet
Dynamic Bayesian Network Inference Using Linear Interactions
function_NonLinearNet
Dynamic Bayesian Network Inference Using Non-Linear...
function_ReplicatesNet_gauss
Dynamic Bayesian Network Inference Using Linear Interactions...
function_ReplicatesNet_student
Dynamic Bayesian Network Inference Using Linear Interactions...
LockeData
Gene expression time series generated with ODE model
LockeDataError
Gene expression time series generated with ODE model with...
plotPriors
Plot prior using parameter vector
readChains
Read MCMC Chains

Files in this package

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