oligo
This is the released version of oligo; for the devel version, see oligo.
Preprocessing tools for oligonucleotide arrays
Bioconductor version: Release (3.23)
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
Author: Benilton Carvalho and Rafael Irizarry
Maintainer: Benilton Carvalho <benilton at unicamp.br>
citation("oligo")):
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("oligo")
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("oligo")| oligo User's Guide | |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, SNP, Software, TwoChannel |
| Version | 1.76.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) (19.5 years) |
| License | LGPL (>= 2) |
| Depends | R (>= 3.2.0), BiocGenerics(>= 0.13.11), oligoClasses(>= 1.29.6), Biobase(>= 2.27.3), Biostrings(>= 2.35.12) |
| Imports | affyio(>= 1.35.0), affxparser(>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore(>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, bit |
| System Requirements | |
| URL | https://github.com/benilton/oligo |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | oligo_1.76.0.tar.gz |
| Windows Binary (x86_64) | oligo_1.76.0.zip |
| macOS Binary (big-sur-x86_64) | oligo_1.76.0.tgz |
| macOS Binary (sonoma-arm64) | oligo_1.76.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/oligo |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/oligo |
| Bioc Package Browser | https://code.bioconductor.org/browse/oligo/ |
| Package Short Url | https://bioconductor.org/packages/oligo/ |
| Package Downloads Report | Download Stats |