DOI: 10.18129/B9.bioc.oligo    

This is the development version of oligo; for the stable release version, see oligo.

Preprocessing tools for oligonucleotide arrays

Bioconductor version: Development (3.17)

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 (from within R, enter citation("oligo")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF oligo User's Guide
PDF   Reference Manual


biocViews DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, SNP, Software, TwoChannel
Version 1.63.0
In Bioconductor since BioC 2.0 (R-2.5) (15.5 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, zlibbioc
LinkingTo preprocessCore
Suggests BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl
Enhances doMC, doMPI
Depends On Me ITALICS, maEndToEnd, pd.atdschip.tiling, pdInfoBuilder, puma, pumadata, SCAN.UPC
Imports Me ArrayExpress, cn.farms, crossmeta, frma, ITALICS, mimager
Suggests Me fastseg, frmaTools, hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package oligo_1.63.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/oligo
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oligo
Package Short Url https://bioconductor.org/packages/oligo/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: