geNetClassifier: Classify diseases and build associated gene networks using gene expression profiles

Share:

Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.

Author
Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.
Date of publication
None
Maintainer
Sara Aibar <saibar@usal.es>
License
GPL (>= 2)
Version
1.14.0
URLs

View on Bioconductor

Man pages

calculateGenesRanking
Calculate GenesRanking
externalValidation.probMatrix
Probability matrix.
externalValidation.stats
Statistics of the external validation.
gClasses-methods
Classes in the ranking.
GeneralizationError-class
Class "GeneralizationError" (slot of GeNetClassifierReturn)
genesDetails-methods
Details of the genes in the network.
GenesNetwork-class
Class "GenesNetwork"
GenesRanking-class
Class "GenesRanking"
geneSymbols
Gene symbols associated to human Ensemble IDs.
geNetClassifier
Main function of the geNetClassifier package. Trains the...
geNetClassifier-package
classify diseases and build associated gene networks using...
GeNetClassifierReturn-class
Class "GeNetClassifierReturn"
getEdges-methods
Edges in the network.
getNodes-methods
Nodes in the network.
getNumEdges-methods
Number of edges in the network.
getNumNodes-methods
Number of nodes in the network.
getRanking-methods
Shows the genes ranking.
getSubNetwork-methods
Get a sub-network.
getTopRanking-methods
Gets a new ranking with the given top genes.
leukemiasClassifier
Sample leukemias classifier
network2txt
network2txt
numGenes-methods
Number of genes in the genesRanking.
numSignificantGenes-methods
Number of ranked genes over the posterior probability...
overview-methods
Overview
plotAssignments
Plot assignment probabilities
plotDiscriminantPower
Plots the genes' Discriminant Power.
plotExpressionProfiles
Expression profiles plot.
plot.GenesRanking
Plot GenesRanking
plot.GeNetClassifierReturn
Plot GeNetClassifierReturn
plotNetwork
Plot GenesNetwork
queryGeNetClassifier
Queries the classifier trained with geNetClassifier.
querySummary
Summary of the query.
setProperties-methods
Set properties

Files in this package

geNetClassifier/DESCRIPTION
geNetClassifier/NAMESPACE
geNetClassifier/NEWS
geNetClassifier/R
geNetClassifier/R/class.GeNetClassifierReturn.R
geNetClassifier/R/class.GeneralizationError.R
geNetClassifier/R/class.GenesNetwork.R
geNetClassifier/R/class.GenesRanking.R
geNetClassifier/R/function.main.R
geNetClassifier/R/functions.private.R
geNetClassifier/R/functions.public.R
geNetClassifier/build
geNetClassifier/build/vignette.rds
geNetClassifier/data
geNetClassifier/data/datalist
geNetClassifier/data/geneSymbols.RData
geNetClassifier/data/leukemiasClassifier.RData
geNetClassifier/inst
geNetClassifier/inst/CITATION
geNetClassifier/inst/doc
geNetClassifier/inst/doc/geNetClassifier-vignette.R
geNetClassifier/inst/doc/geNetClassifier-vignette.Rnw
geNetClassifier/inst/doc/geNetClassifier-vignette.pdf
geNetClassifier/inst/unitTests
geNetClassifier/inst/unitTests/test_externalValidationStats.R
geNetClassifier/inst/unitTests/test_geNetClassifier.R
geNetClassifier/inst/unitTests/test_plotExpressionProfiles.R
geNetClassifier/man
geNetClassifier/man/GeNetClassifierReturn-class.Rd
geNetClassifier/man/GeneralizationError-class.Rd
geNetClassifier/man/GenesNetwork-class.Rd
geNetClassifier/man/GenesRanking-class.Rd
geNetClassifier/man/calculateGenesRanking.Rd
geNetClassifier/man/externalValidation.probMatrix.Rd
geNetClassifier/man/externalValidation.stats.Rd
geNetClassifier/man/gClasses-methods.Rd
geNetClassifier/man/geNetClassifier-package.Rd
geNetClassifier/man/geNetClassifier.Rd
geNetClassifier/man/geneSymbols.Rd
geNetClassifier/man/genesDetails-methods.Rd
geNetClassifier/man/getEdges-methods.Rd
geNetClassifier/man/getNodes-methods.Rd
geNetClassifier/man/getNumEdges-methods.Rd
geNetClassifier/man/getNumNodes-methods.Rd
geNetClassifier/man/getRanking-methods.Rd
geNetClassifier/man/getSubNetwork-methods.Rd
geNetClassifier/man/getTopRanking-methods.Rd
geNetClassifier/man/leukemiasClassifier.Rd
geNetClassifier/man/network2txt.Rd
geNetClassifier/man/numGenes-methods.Rd
geNetClassifier/man/numSignificantGenes-methods.Rd
geNetClassifier/man/overview-methods.Rd
geNetClassifier/man/plot.GeNetClassifierReturn.Rd
geNetClassifier/man/plot.GenesRanking.Rd
geNetClassifier/man/plotAssignments.Rd
geNetClassifier/man/plotDiscriminantPower.Rd
geNetClassifier/man/plotExpressionProfiles.Rd
geNetClassifier/man/plotNetwork.Rd
geNetClassifier/man/queryGeNetClassifier.Rd
geNetClassifier/man/querySummary.Rd
geNetClassifier/man/setProperties-methods.Rd
geNetClassifier/tests
geNetClassifier/tests/runTests.R
geNetClassifier/vignettes
geNetClassifier/vignettes/Fig11plotNtwALL9g.png
geNetClassifier/vignettes/Fig12plotNtwAML30g.png
geNetClassifier/vignettes/Fig13plotNtwAML100g.pdf
geNetClassifier/vignettes/Fig1intro.png
geNetClassifier/vignettes/Fig2significantGeneswithoutNoL.pdf
geNetClassifier/vignettes/Fig3overlap.png
geNetClassifier/vignettes/Fig4-5geneSelection.pdf
geNetClassifier/vignettes/Fig6leukemiasClassifierAssingorNotAssing.pdf
geNetClassifier/vignettes/Fig7significantGenes.pdf
geNetClassifier/vignettes/Fig8expressionProfilePlot_2g.pdf
geNetClassifier/vignettes/Fig9expressionProfilePlot_B.pdf
geNetClassifier/vignettes/geNetClassifier-vignette.Rnw