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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("oligo")

To cite this package in a publication, start R and enter:

    citation("oligo")

Documentation

PDF R Script 01 - Overview
PDF R Script 02 - NimbleGen Expression and Preprocessing
PDF R Script 03 - SNP Chips and Genotyping
PDF R Script 04 - Experimental Features
PDF R Script 05 - Exon ST and Gene ST Arrays
PDF   Reference Manual

Details

biocViews Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
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
Suggests hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData
System Requirements
License LGPL (>= 2)
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
Version 1.16.2
Since Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source oligo_1.16.2.tar.gz
Windows Binary oligo_1.16.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary oligo_1.16.2.tgz
Package Downloads Report Download Stats

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