oligo

Preprocessing tools for oligonucleotide arrays.

Bioconductor version: Development (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, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber

Maintainer: Benilton Carvalho

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("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

Reference Manual

Details

biocViews	Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland
Depends	R, oligoClasses, preprocessCore
Imports	affyio, affxparser, Biobase, Biostrings, DBI, 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, pdInfoBuilder
Imports Me	ITALICS, charm, cn.farms, frma, makePlatformDesign
Suggests Me	frmaTools
Version	1.15.11

Package Downloads

Package Source	oligo_1.15.11.tar.gz
Windows Binary	oligo_1.15.9.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	oligo_1.15.9.tgz
Package Downloads Report	Download Stats