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.

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
http://julien.cremeriefamily.info/simone.html

View on CRAN

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.