To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("oligo")

In most cases, you don't need to download the package archive at all.

oligo

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see oligo.

Preprocessing tools for oligonucleotide arrays.

Bioconductor version: 2.8

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 <Benilton.Carvalho at cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber

Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("oligo")

Documentation

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

browseVignettes("oligo")

PDF		V1Overview.pdf
PDF		V2NExpression.pdf
PDF		V3AffySnpGenotype.pdf
PDF		V4Experimental.pdf
PDF		V5ExonGene.pdf
PDF		Reference Manual

Details

biocViews	Bioinformatics, ChIPchip, CopyNumberVariants, CpGIsland, DNAMethylation, DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, SNP, Software, Transcription, TwoChannel
Version	1.16.2
In Bioconductor since	BioC 2.0 (R-2.5) (9 years)
License	LGPL (>= 2)
Depends	R (>= 2.13.0), oligoClasses(>= 1.13.9), preprocessCore(>= 1.13.5)
Imports	affyio(>= 1.19.4), affxparser(>= 1.23.1), Biobase(>= 2.11.8), Biostrings, DBI (>= 0.2-5), ff, graphics, methods, splines, stats, utils
LinkingTo	preprocessCore
Suggests	hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData
SystemRequirements
Enhances	ff, snow
URL
Depends On Me	ITALICS, oligoData, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter, pd.ag, pd.barley1, pd.bovine, pd.bsubtilis, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken, pd.citrus, pd.cotton, pd.cytogenetics.array, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mouse430.2, pd.mouse430a.2, pd.mu11ksuba, pd.mu11ksubb, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.rat230.2, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhesus, pd.rice, pd.rn.u34, pd.s.aureus, pd.soybean, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebrafish, pdInfoBuilder
Imports Me	charm, cn.farms, frma, ITALICS, makePlatformDesign
Suggests Me	frmaTools, hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex
Build Report

Package Archives

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

Package Source	oligo_1.16.2.tar.gz
Windows Binary	oligo_1.16.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/oligo/tree/release-2.8
Package Short Url	http://bioconductor.org/packages/oligo/
Package Downloads Report	Download Stats