biosigner
This is the released version of biosigner; for the devel version, see biosigner.
Signature discovery from omics data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| biosigner-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, FeatureExtraction, Lipidomics, MassSpectrometry, Metabolomics, Proteomics, Software, Transcriptomics |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 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 | BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | biosigner_1.40.0.tar.gz |
| Windows Binary (x86_64) | biosigner_1.40.0.zip |
| macOS Binary (big-sur-x86_64) | biosigner_1.40.0.tgz |
| macOS Binary (sonoma-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 |