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biosigner

Signature discovery from omics data


Bioconductor version: Release (3.18)

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 [aut], Etienne A. Thevenot [aut, cre]

Maintainer: Etienne A. Thevenot <etienne.thevenot at cea.fr>

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

Installation

To install this package, start R (version "4.3") 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")
biosigner-vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, FeatureExtraction, Lipidomics, MassSpectrometry, Metabolomics, Proteomics, Software, Transcriptomics
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License CeCILL
Depends
Imports Biobase, methods, e1071, grDevices, graphics, MultiAssayExperiment, MultiDataSet, randomForest, ropls, stats, SummarizedExperiment, utils
System Requirements
URL http://dx.doi.org/10.3389/fmolb.2016.00026
See More
Suggests BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me multiSight
Suggests Me phenomis
Links To Me
Build Report Build Report

Package Archives

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

Source Package biosigner_1.30.0.tar.gz
Windows Binary biosigner_1.30.0.zip (64-bit only)
macOS Binary (x86_64) biosigner_1.30.0.tgz
macOS Binary (arm64)
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