CNORfeeder: Integration of CellNOptR to add missing links

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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.

Author
F.Eduati
Date of publication
None
Maintainer
F.Eduati <eduati@ebi.ac.uk>
License
GPL-3
Version
1.14.0

View on Bioconductor

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.

Files in this package

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