geneRecommender
This is the development version of geneRecommender; for the stable release version, see geneRecommender.
A gene recommender algorithm to identify genes coexpressed with a query set of genes
Bioconductor version: Development (3.24)
This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.
Author: Gregory J. Hather <ghather at gmail.com>, with contributions from Art B. Owen <art at stat.stanford.edu> and Terence P. Speed <terry at stat.berkeley.edu>
Maintainer: Greg Hather <ghather at gmail.com>
citation("geneRecommender")):
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("geneRecommender")
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("geneRecommender")| Using the geneRecommender Package | R Script | |
| Reference Manual |
Details
| biocViews | Clustering, Microarray, Software |
| Version | 1.85.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | GPL (>= 2) |
| Depends | R (>= 1.8.0), Biobase(>= 1.4.22), methods |
| Imports | Biobase, methods, stats |
| System Requirements | |
| URL |
See More
| Suggests | |
| 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 | geneRecommender_1.85.0.tar.gz |
| Windows Binary (x86_64) | geneRecommender_1.85.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | geneRecommender_1.85.0.tgz |
| macOS Binary (sonoma-arm64) | geneRecommender_1.85.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/geneRecommender |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/geneRecommender |
| Bioc Package Browser | https://code.bioconductor.org/browse/geneRecommender/ |
| Package Short Url | https://bioconductor.org/packages/geneRecommender/ |
| Package Downloads Report | Download Stats |