oligo

Tools for low-level analysis of oligonucleotide arrays.

Bioconductor version: 2.5

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.

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	Analysis of NimbleGen Expression Data with the oligo Package
PDF	R Script	Classes Used in the Oligo Packages
PDF	R Script	Oligo Vignette
PDF		Reference Manual

Details

biocViews	Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
Depends	R (>= 2.10.0), oligoClasses(>= 1.7.12), preprocessCore(>= 1.7.4)
Imports	splines, affxparser(>= 1.17.3), graphics, utils, stats, DBI (>= 0.2-4), Biobase(>= 2.5.5), methods, affyio(>= 1.13.3)
Suggests	hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer
System Requirements
License	LGPL (>= 2)
URL
Depends On Me	ITALICS, makePlatformDesign, pdInfoBuilder
Imports Me
Suggests Me	hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex, oligoClasses
Version	1.10.4
Since	Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source	oligo_1.10.4.tar.gz
Windows Binary	oligo_1.10.4.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	oligo_1.10.4.tgz
Package Downloads Report	Download Stats

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