simone: Statistical Inference for MOdular NEtworks (SIMoNe)
Version 1.0-3

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.

AuthorJulien 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 publication2016-01-23 00:27:46
MaintainerJulien Chiquet <julien.chiquet@genopole.cnrs.fr>
LicenseGPL (>= 2)
Version1.0-3
URL http://julien.cremeriefamily.info/simone.html
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("simone")

Getting started

Package overview

Popular 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.network: Graphical representation of a network
rNetwork: Simulation of (clustered) Gaussian networks
rTranscriptData: Simulation of artificial transcriptomic data
simone: SIMoNe algorithm for network inference
See all...

All man pages Function index File listing

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)

Functions

CoopLassoConstraint Man page Source code
Gplot Man page Source code
Gplot.add Man page Source code
Gplot.default Man page Source code
Gplot.delete Man page Source code
Gplot.edge Man page Source code
Gplot.graphics Man page Source code
Gplot.inference Man page
Gplot.network Man page Source code
Gplot.pie.nodes Man page Source code
Gplot.radial.vertex.label Man page Source code
Gplot.vertex Man page Source code
Gplot.vertex.label Man page Source code
Gplot.vertex.pie Man page Source code
GroupLassoConstraint Man page Source code
InferEdges Man page Source code
InferStructure Man page Source code
L1 Man page Source code
L2 Man page Source code
L3 Man page Source code
LassoConstraint Man page Source code
OptInference Man page Source code
analysis Man page Source code
cancer Man page
coNetwork Man page Source code
color.lightening Man page Source code
dL1 Man page Source code
dL2 Man page Source code
dL3 Man page Source code
default.color.map Source code
draw.arc Man page Source code
draw.circle Man page Source code
draw.edges Man page Source code
draw.loops Man page Source code
draw.rot.poly Man page Source code
draw.sector Man page Source code
get.rho.max Man page Source code
getDegree Man page Source code
getNetwork Man page Source code
graphical.lasso Man page Source code
is.simone Man page Source code
is.simone.network Man page Source code
is.symetric Man page Source code
isolate.vertices Man page Source code
laplacian Man page Source code
light.palette Man page Source code
multiple.dynamic Man page Source code
multiple.static Man page Source code
nb.edges Man page Source code
neighborhood.selection Man page Source code
onAttach Source code
onLoad Source code
plot.AIC Man page Source code
plot.BIC Man page Source code
plot.PR Man page Source code
plot.ROC Man page Source code
plot.path Man page Source code
plot.sequence Man page Source code
plot.simone Man page Source code
plot.simone.network Man page Source code
rNetwork Man page Source code
rTranscriptData Man page Source code
setOptions Man page Source code
simone Man page Source code
simone-package Man page
sub.param Man page Source code
var1.inference Man page Source code

Files

inst
inst/CITATION
src
src/inference_algos.c
src/vertex_layout.c
src/inference_utils.h
src/matrix.h
NAMESPACE
demo
demo/check_glasso.R
demo/simone_timeCourse.R
demo/cancer_multitask.R
demo/simone_steadyState.R
demo/simone_multitask.R
demo/cancer_pooled.R
demo/00Index
NEWS
data
data/cancer.rdata
R
R/plot.simone.R
R/init.R
R/simone.R
R/plot.simone.network.R
R/Gplot-internals.R
R/SimData.R
R/InferEdges-internals.R
R/Gplot.R
R/InferEdges.R
R/InferClasses.R
MD5
DESCRIPTION
man
man/simone.Rd
man/setOptions.Rd
man/simone-internal.Rd
man/plot.simone.Rd
man/rNetwork.Rd
man/coNetwork.Rd
man/simone-package.Rd
man/data-cancer.Rd
man/rTranscriptData.Rd
man/getNetwork.Rd
man/plot.simone.network.Rd
simone documentation built on May 19, 2017, 8:32 a.m.

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