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DOI: 10.18129/B9.bioc.oligo    

Preprocessing tools for oligonucleotide arrays

Bioconductor version: Release (3.5)

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>

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


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PDF oligo User's Guide
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, SNP, Software, TwoChannel
Version 1.40.2
In Bioconductor since BioC 2.0 (R-2.5) (10.5 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.hg18.60mer.expr,, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, GenomeGraphs, RCurl, ACME, biomaRt, AnnotationDbi, GenomeGraphs, RCurl
Enhances ff, doMC, doMPI
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.atdschip.tiling, pd.ath1.121501, pd.barley1,,, pd.bovine, pd.bsubtilis,,, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken,,,,, pd.citrus, pd.clariom.d.human, pd.clariom.s.human,, pd.clariom.s.mouse,, pd.clariom.s.rat,, pd.cotton,,,,, pd.cytogenetics.array,,, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2,,,,,,,,,,, pd.genomewidesnp.5, pd.genomewidesnp.6,,, pd.hc.g110, pd.hg.focus,, 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.hg18.60mer.expr,,,, pd.hta.2.0, pd.hu6800,,,,,, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240,,,,, pd.medicago,,,,,,, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.3.1, pd.mirna.4.0, pd.moe430a, pd.moe430b,,,,,, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177,,, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine,,,,, pd.rae230a, pd.rae230b,,,,,, pd.rat230.2,,, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c,,, pd.rhesus, pd.rice,,, pd.rn.u34, pd.rta.1.0,,, 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, puma, pumadata, SCAN.UPC, waveTiling
Imports Me ArrayExpress, charm, cn.farms, crossmeta, frma, ITALICS, mimager
Suggests Me BiocGenerics, fastseg, frmaTools, hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex
Build Report  

Package Archives

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

Source Package oligo_1.40.2.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) oligo_1.40.2.tgz
Source Repository git clone
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