CNORfeeder: Integration of CellNOptR to add missing links
Version 1.16.0

This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.

AuthorF.Eduati
Bioconductor views Bioinformatics CellBasedAssays CellBiology NetworkInference Proteomics
Date of publicationNone
MaintainerF.Eduati <eduati@ebi.ac.uk>
LicenseGPL-3
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CNORfeeder")

Getting started

Package overview

Popular man pages

Binference: Bayesian network inference
CNORfeeder-package: R package to integrate literature-constrained and data-driven...
mapDDN2model: Integrate data-drive network with the model
MIinference: Mutual information based network inference
PPINigraph: Protein-protein interaction netwrok
UniprotIDdream: Uniprot identifiers for proteins in DreamModel
weighting: Weight integrated links.
See all...

All man pages Function index File listing

Man pages

Binference: Bayesian network inference
CNORfeeder-package: R package to integrate literature-constrained and data-driven...
gaBinaryT1W: Genetic algorithm used to optimise a model differently...
linksRanking: Ranking of links inferred from data
makeBTables: Make Boolean tables
mapBTables2model: Integrate Boolean tables with the model
mapDDN2model: Integrate data-drive network with the model
MIinference: Mutual information based network inference
PPINigraph: Protein-protein interaction netwrok
UniprotIDdream: Uniprot identifiers for proteins in DreamModel
weighting: Weight integrated links.

Functions

Binference Man page Source code
CNORfeeder Man page
CNORfeeder-package Man page
MIinference Man page Source code
PPINigraph Man page
UniprotIDdream Man page
addLink Source code
addLinkAND Source code
addPriorKnowledge Source code
computeScoreT1W Source code
cutModelW Source code
downCueGraph Source code
fillHashTable Source code
gaBinaryT1W Man page Source code
getFitW Source code
linksRanking Man page Source code
makeBTables Man page Source code
mapBTables2model Man page Source code
mapDDN2model Man page Source code
searchLinkGraph Source code
searchPPIigraph Source code
shift Source code
upSignalGraph Source code
weighting Man page Source code

Files

ChangeLog.txt
DESCRIPTION
NAMESPACE
R
R/Binference.R
R/MIinference.R
R/addLink.R
R/addLinkAND.R
R/computeScoreT1W.R
R/cutModelW.R
R/downCueGraph.R
R/gaBinaryT1W.R
R/getFitW.R
R/linksRanking.R
R/makeBTables.R
R/mapBTables2model.R
R/mapDDN2model.R
R/searchLinkGraph.R
R/searchPPIigraph.R
R/upSignalGraph.R
R/weighting.R
build
build/vignette.rds
data
data/PPINigraph.RData
data/UniprotIDdream.RData
inst
inst/NEWS.Rd
inst/doc
inst/doc/CNORfeeder-vignette.R
inst/doc/CNORfeeder-vignette.Rnw
inst/doc/CNORfeeder-vignette.pdf
inst/unitTests
inst/unitTests/test_inference.R
inst/unitTests/test_integration.R
inst/unitTests/test_weighting.R
man
man/Binference.Rd
man/CNORfeeder-package.Rd
man/MIinference.Rd
man/PPINigraph.Rd
man/UniprotIDdream.Rd
man/gaBinaryT1W.Rd
man/linksRanking.Rd
man/makeBTables.Rd
man/mapBTables2model.Rd
man/mapDDN2model.Rd
man/weighting.Rd
tests
tests/runTests.R
vignettes
vignettes/CNORfeeder-vignette.Rnw
vignettes/DDN.pdf
vignettes/Figure1.png
vignettes/SimResultsT1_1.pdf
vignettes/integratedModel.pdf
vignettes/optModel.pdf
CNORfeeder documentation built on May 20, 2017, 10:39 p.m.

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