lpNet: Linear Programming Model for Network Inference

lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.

AuthorBettina Knapp, Marta R. A. Matos, Johanna Mazur, Lars Kaderali
Date of publicationNone
MaintainerLars Kaderali <lars.kaderali@tu-dresden.de>
LicenseArtistic License 2.0
Version2.6.0

View on Bioconductor

Files

lpNet/DESCRIPTION
lpNet/NAMESPACE
lpNet/R
lpNet/R/calcActivation.R lpNet/R/calcPredictionKfoldCV.R lpNet/R/calcPredictionLOOCV.R lpNet/R/calcRangeLambda.R lpNet/R/doILP.R lpNet/R/doILP_steadyState.R lpNet/R/doILP_timeSeries.R
lpNet/R/generateTimeSeriesNetStates.r
lpNet/R/getAdja.R lpNet/R/getBaseline.R lpNet/R/getEdgeAnnot.R lpNet/R/getObsMat.R lpNet/R/getSampleAdja.R lpNet/R/getSampleAdjaMAD.R lpNet/R/kfoldCV.R lpNet/R/loocv.R lpNet/R/summarizeRepl.R
lpNet/build
lpNet/build/vignette.rds
lpNet/inst
lpNet/inst/NEWS
lpNet/inst/doc
lpNet/inst/doc/vignette_lpNet.R
lpNet/inst/doc/vignette_lpNet.Rnw
lpNet/inst/doc/vignette_lpNet.pdf
lpNet/man
lpNet/man/CV.Rd lpNet/man/calcActivation.Rd lpNet/man/calcPrediction.Rd lpNet/man/calcRangeLambda.Rd lpNet/man/doILP.Rd lpNet/man/generateTimeSeriesNetStates.Rd lpNet/man/getAdja.Rd lpNet/man/getBaseline.Rd lpNet/man/getEdgeAnnot.Rd lpNet/man/getObsMat.Rd lpNet/man/getSampleAdja.Rd lpNet/man/lpNet-package.Rd lpNet/man/summarizeRepl.Rd
lpNet/tests
lpNet/tests/runitCalcActivation.R
lpNet/tests/runitCalcPredictionKfoldCV.R
lpNet/tests/runitCalcPredictionKfoldCV_timeSeries.R
lpNet/tests/runitCalcPredictionLOOCV.R
lpNet/tests/runitCalcPredictionLOOCV_timeSeries.R
lpNet/tests/runitCalcRangeLambda.R
lpNet/tests/runitDoILP.R
lpNet/tests/runitDoILP_timeSeries.R
lpNet/tests/runitGenerateTimeSeriesNetStates.R
lpNet/tests/runitGetAdja.R
lpNet/tests/runitGetBaseline.R
lpNet/tests/runitGetEdgeAnnot.R
lpNet/tests/runitGetObsMat.R
lpNet/tests/runitGetSampleAdja.R
lpNet/tests/runitGetSampleAdjaMAD.R
lpNet/tests/runitKfoldCV.R
lpNet/tests/runitKfoldCV_timeSeries.R
lpNet/tests/runitLOOCV.R
lpNet/tests/runitLOOCV_timeSeries.R
lpNet/vignettes
lpNet/vignettes/references.bib
lpNet/vignettes/vignette_lpNet.Rnw

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