biosigner: Signature discovery from omics data

Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets. A Galaxy implementation of the package is available within the Workflow4metabolomics.org online infrastructure for computational metabolomics.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("biosigner")
AuthorPhilippe Rinaudo <phd.rinaudo@gmail.com>, Etienne Thevenot <etienne.thevenot@cea.fr>
Bioconductor views Classification FeatureExtraction Lipidomics Metabolomics Proteomics Transcriptomics
Date of publicationNone
MaintainerPhilippe Rinaudo <phd.rinaudo@gmail.com>, Etienne Thevenot <etienne.thevenot@cea.fr>
LicenseCeCILL
Version1.2.4

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/allClasses.R R/allGenerics.R R/biosigner-package.R R/datasets.R R/helpers.R R/methods.R
build
build/vignette.rds
data
data/datalist
data/diaplasma.rdata
inst
inst/CITATION
inst/doc
inst/doc/biosigner-vignette.R
inst/doc/biosigner-vignette.Rmd
inst/doc/biosigner-vignette.pdf
inst/unitTests
inst/unitTests/test_biosigner.R
man
man/biosign-class.Rd man/biosign.Rd man/biosigner-package.Rd man/diaplasma.Rd man/getAccuracyMN.Rd man/getSignatureLs.Rd man/plot.Rd man/predict.Rd man/show.Rd
tests
tests/runTests.R
vignettes
vignettes/biosigner-vignette.Rmd
vignettes/biosigner-vignette.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.