predictionet: Inference for predictive networks designed for (but not limited to) genomic data

This package contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases. The main function is able to generate networks using Bayesian or regression-based inference methods; while the former is limited to < 100 of variables, the latter may infer networks with hundreds of variables. Several statistics at the edge and node levels have been implemented (edge stability, predictive ability of each node, ...) in order to help the user to focus on high quality subnetworks. Ultimately, this package is used in the 'Predictive Networks' web application developed by the Dana-Farber Cancer Institute in collaboration with Entagen.

AuthorBenjamin Haibe-Kains, Catharina Olsen, Gianluca Bontempi, John Quackenbush
Date of publicationNone
MaintainerBenjamin Haibe-Kains <bhaibeka@jimmy.harvard.edu>, Catharina Olsen <colsen@ulb.ac.be>
LicenseArtistic-2.0
Version1.20.0
http://compbio.dfci.harvard.edu
http://www.ulb.ac.be/di/mlg

View on Bioconductor

Functions

adj.get.hops Man page
adj.remove.cycles Man page
annot2.ras Man page
annot.ras Man page
data2.ras Man page
data.discretize Man page
data.ras Man page
demo2.ras Man page
demo.ras Man page
eval.network Man page
expO.colon.ras Man page
jorissen.colon.ras Man page
mcc Man page
net2pred Man page
netinf Man page
netinf2gml Man page
netinf.cv Man page
netinf.predict Man page
predictionet Man page
predictionet-package Man page
predictionet.press.statistic Man page
predictionet.stability.cv Man page
pred.score Man page
priors2.ras Man page
priors.ras Man page

Files

predictionet/.BBSoptions
predictionet/DESCRIPTION
predictionet/NAMESPACE
predictionet/R
predictionet/R/adj.get.hops.R predictionet/R/adj.remove.cycles.R predictionet/R/build.regression.regrnet.R predictionet/R/build2.mim.R predictionet/R/data.discretize.R predictionet/R/eval.network.R predictionet/R/exportGML.R predictionet/R/extract.adjacency.ensemble.R predictionet/R/extract.all.parents.R predictionet/R/fit.catnet.R predictionet/R/fit.regrnet.causal.R predictionet/R/fit.regrnet.causal.ensemble.R predictionet/R/fit.regrnet.causal2.R predictionet/R/get.ii4triplets.gaussian.R predictionet/R/list2matrixens.R predictionet/R/mcc.R predictionet/R/net2pred.R predictionet/R/netinf.R predictionet/R/netinf.cv.R predictionet/R/netinf.predict.R predictionet/R/netinf2gml.R predictionet/R/network2triplets.R predictionet/R/pred.onegene.bayesnet.fs.R predictionet/R/pred.onegene.regrnet.fs.R predictionet/R/pred.score.R predictionet/R/pred2mean.R predictionet/R/predictionet.press.statistic.R predictionet/R/predictionet.stability.cv.R predictionet/R/rank.genes.causal.ensemble.R predictionet/R/rank.genes.causal.perturbations.R predictionet/R/rank.genes.causal.perturbations2.R predictionet/R/rank.genes.ensemble.R predictionet/R/regrlin.R predictionet/R/regrnet2matrixtopo.R predictionet/R/stab.cv2stab.R predictionet/R/topo2stab.R
predictionet/README
predictionet/build
predictionet/build/predictionet.pdf
predictionet/build/vignette.rds
predictionet/data
predictionet/data/datalist
predictionet/data/expO.colon.ras.rda
predictionet/data/jorissen.colon.ras.rda
predictionet/inst
predictionet/inst/doc
predictionet/inst/doc/predictionet.R
predictionet/inst/doc/predictionet.Rnw
predictionet/inst/doc/predictionet.pdf
predictionet/inst/extdata
predictionet/inst/extdata/bild2006_ras_signature_348.csv
predictionet/inst/extdata/preditionet_vizmap1.props
predictionet/inst/extdata/preditionet_vizmap2.props
predictionet/inst/extdata/priors_ras_bild2006_pnwebapp.csv
predictionet/man
predictionet/man/adj.get.hops.Rd predictionet/man/adj.remove.cycles.Rd predictionet/man/data.discretize.Rd predictionet/man/eval.network.Rd predictionet/man/expO.colon.ras.Rd predictionet/man/jorissen.colon.ras.Rd predictionet/man/mcc.Rd predictionet/man/net2pred.Rd predictionet/man/netinf.Rd predictionet/man/netinf.cv.Rd predictionet/man/netinf.predict.Rd predictionet/man/netinf2gml.Rd predictionet/man/pred.score.Rd predictionet/man/predictionet-package.Rd predictionet/man/predictionet.press.statistic.Rd predictionet/man/predictionet.stability.cv.Rd
predictionet/src
predictionet/src/foo_mrmr.cpp
predictionet/src/foo_mrmr.h
predictionet/src/mrnet_adapted.cpp
predictionet/src/mrnet_adapted2.cpp
predictionet/src/mrnet_ensemble_standalone.cpp
predictionet/src/tree.h
predictionet/vignettes
predictionet/vignettes/biblio.bib
predictionet/vignettes/predictionet-cytoscape.pdf
predictionet/vignettes/predictionet-pn_webapp_ras.pdf
predictionet/vignettes/predictionet-regrnet_design.pdf
predictionet/vignettes/predictionet.Rnw

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