biosigner

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see biosigner.

Signature discovery from omics data


Bioconductor version: 3.10

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.

Author: Philippe Rinaudo <phd.rinaudo at gmail.com>, Etienne Thevenot <etienne.thevenot at cea.fr>

Maintainer: Philippe Rinaudo <phd.rinaudo at gmail.com>, Etienne Thevenot <etienne.thevenot at cea.fr>

Citation (from within R, enter citation("biosigner")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("biosigner")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("biosigner")
Vignette Title HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, FeatureExtraction, Lipidomics, Metabolomics, Proteomics, Software, Transcriptomics
Version 1.14.4
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License CeCILL
Depends Biobase, ropls
Imports methods, e1071, MultiDataSet, randomForest
System Requirements
URL
See More
Suggests BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package biosigner_1.14.4.tar.gz
Windows Binary biosigner_1.14.4.zip
Mac OS X 10.11 (El Capitan) biosigner_1.14.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/biosigner
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/biosigner
Bioc Package Browser https://code.bioconductor.org/browse/biosigner/
Package Short Url https://bioconductor.org/packages/biosigner/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive