geNetClassifier
This is the released version of geNetClassifier; for the devel version, see geNetClassifier.
Classify diseases and build associated gene networks using gene expression profiles
Bioconductor version: Release (3.23)
Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.
Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.
Maintainer: Sara Aibar <saibar at usal.es>
citation("geNetClassifier")):
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("geNetClassifier")
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("geNetClassifier")| geNetClassifier-vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, DifferentialExpression, Microarray, Software |
| Version | 1.52.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.1), Biobase(>= 2.5.5), EBarrays, minet, methods |
| Imports | e1071, graphics, grDevices |
| System Requirements | |
| URL | http://www.cicancer.org |
See More
| Suggests | leukemiasEset, RUnit, BiocGenerics |
| Linking To | |
| Enhances | RColorBrewer, igraph, infotheo |
| Depends On Me | |
| Imports Me | bioCancer, canceR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | geNetClassifier_1.52.0.tar.gz |
| Windows Binary (x86_64) | geNetClassifier_1.52.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | geNetClassifier_1.52.0.tgz |
| macOS Binary (sonoma-arm64) | geNetClassifier_1.52.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/geNetClassifier |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/geNetClassifier |
| Bioc Package Browser | https://code.bioconductor.org/browse/geNetClassifier/ |
| Package Short Url | https://bioconductor.org/packages/geNetClassifier/ |
| Package Downloads Report | Download Stats |