oligo

Preprocessing tools for oligonucleotide arrays.

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

Documentation

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
Reference Manual

Details

biocViews	Microarray , OneChannel , TwoChannel , Preprocessing , SNP , DifferentialExpression , DNAMethylation , ExonArray , GeneExpression , Bioinformatics , DataImport , Transcription , ChIPchip , CopyNumberVariants , CpGIsland
Depends	R , oligoClasses
Imports	affyio , affxparser , Biobase , DBI , graphics , methods , preprocessCore , 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 , pdInfoBuilder
Imports Me	charm , makePlatformDesign
Suggests Me

Package Downloads

Package source	oligo_1.12.2.tar.gz
Windows 32-bit binary	oligo_1.12.2.zip
Windows 64-bit binary	oligo_1.12.2.zip
MacOS X 10.5 (Leopard) binary	oligo_1.12.2.tgz
Package Downloads Report	Downloads Stats