simone: Statistical Inference for MOdular NEtworks (SIMoNe)

Implements the inference of co-expression networks based on partial correlation coefficients from either steady-state or time-course transcriptomic data. Note that with both type of data this package can deal with samples collected in different experimental conditions and therefore not identically distributed. In this particular case, multiple but related networks are inferred on one simone run.

Author
Julien Chiquet <julien.chiquet@genopole.cnrs.fr>, Gilles Grasseau <gilles.grasseau@genopole.cnrs.fr>, Camille Charbonnier <camille.charbonnier@genopole.cnrs.fr>, Christophe Ambroise <christophe.ambroise@genopole.cnrs.fr>.
Date of publication
2016-01-23 00:27:46
Maintainer
Julien Chiquet <julien.chiquet@genopole.cnrs.fr>
License
GPL (>= 2)
Version
1.0-3
URLs

View on CRAN

Man pages

coNetwork
Random perturbations of a reference network
data-cancer
Microarray data set for breast cancer
getNetwork
Network extraction from a SIMoNe run
plot.simone
Graphical representation of SIMoNe outputs
plot.simone.network
Graphical representation of a network
rNetwork
Simulation of (clustered) Gaussian networks
rTranscriptData
Simulation of artificial transcriptomic data
setOptions
Low-level options of a SIMoNe run
simone
SIMoNe algorithm for network inference
simone-internal
'simone' internal functions
simone-package
Statistical Inference for MOdular NEtworks (SIMoNe)

Files in this package

simone
simone/inst
simone/inst/CITATION
simone/src
simone/src/inference_algos.c
simone/src/vertex_layout.c
simone/src/inference_utils.h
simone/src/matrix.h
simone/NAMESPACE
simone/demo
simone/demo/check_glasso.R
simone/demo/simone_timeCourse.R
simone/demo/cancer_multitask.R
simone/demo/simone_steadyState.R
simone/demo/simone_multitask.R
simone/demo/cancer_pooled.R
simone/demo/00Index
simone/NEWS
simone/data
simone/data/cancer.rdata
simone/R
simone/R/plot.simone.R
simone/R/init.R
simone/R/simone.R
simone/R/plot.simone.network.R
simone/R/Gplot-internals.R
simone/R/SimData.R
simone/R/InferEdges-internals.R
simone/R/Gplot.R
simone/R/InferEdges.R
simone/R/InferClasses.R
simone/MD5
simone/DESCRIPTION
simone/man
simone/man/simone.Rd
simone/man/setOptions.Rd
simone/man/simone-internal.Rd
simone/man/plot.simone.Rd
simone/man/rNetwork.Rd
simone/man/coNetwork.Rd
simone/man/simone-package.Rd
simone/man/data-cancer.Rd
simone/man/rTranscriptData.Rd
simone/man/getNetwork.Rd
simone/man/plot.simone.network.Rd