biosigner
Signature discovery from omics data
Bioconductor version: Release (3.20)
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("biosigner")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, FeatureExtraction, Lipidomics, MassSpectrometry, Metabolomics, Proteomics, Software, Transcriptomics |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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 | |
| 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | biosigner_1.34.0.zip |
| macOS Binary (x86_64) | biosigner_1.34.0.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 |