Rmagpie
This is the development version of Rmagpie; for the stable release version, see Rmagpie.
MicroArray Gene-expression-based Program In Error rate estimation
Bioconductor version: Development (3.24)
Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.
Author: Camille Maumet <Rmagpie at gmail.com>, with contributions from C. Ambroise J. Zhu
Maintainer: Camille Maumet <Rmagpie at gmail.com>
citation("Rmagpie")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Rmagpie")
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("Rmagpie")| Rmagpie Examples | R Script | |
| Reference Manual |
Details
| biocViews | Classification, Microarray, Software |
| Version | 1.69.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (17.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 2.6.1), Biobase(>= 2.5.5) |
| Imports | Biobase(>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils |
| System Requirements | |
| URL | http://www.bioconductor.org/ |
See More
| Suggests | xtable |
| 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 | Rmagpie_1.69.0.tar.gz |
| Windows Binary (x86_64) | Rmagpie_1.69.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Rmagpie_1.69.0.tgz |
| macOS Binary (sonoma-arm64) | Rmagpie_1.69.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rmagpie |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rmagpie |
| Bioc Package Browser | https://code.bioconductor.org/browse/Rmagpie/ |
| Package Short Url | https://bioconductor.org/packages/Rmagpie/ |
| Package Downloads Report | Download Stats |