oligo

Preprocessing tools for oligonucleotide arrays.

Bioconductor version: 2.6

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 <carvalho at bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber

Maintainer: Benilton Carvalho <carvalho at bclab.org>

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		Reference Manual

Details

biocViews	Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
Depends	R (>= 2.11.0), oligoClasses(>= 1.9.41)
Imports	affyio(>= 1.15.2), affxparser(>= 1.17.3), Biobase(>= 2.7.3), DBI (>= 0.2-4), graphics, methods, preprocessCore(>= 1.9.0), splines, stats, utils
Suggests	hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
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.charm.hg18.example, pd.cytogenetics.array, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.hg.u95a, pd.hg.u95av2, pd.ht.hg.u133.plus.pm, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mouse430.2, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pdInfoBuilder
Imports Me	charm, makePlatformDesign
Suggests Me	hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex
Version	1.12.2
Since	Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source	oligo_1.12.2.tar.gz
Windows Binary	oligo_1.12.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	oligo_1.12.2.tgz
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