Ringo

R Investigation of ChIP-chip Oligoarrays

Bioconductor version: Development (2.8)

The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities.

Author: Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber

Maintainer: J. Toedling

To install this package, start R and enter:

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

Documentation

PDF	R Script	R Investigation of NimbleGen Oligoarrays
PDF		Rplots.pdf

Reference Manual

Details

biocViews	Microarray, TwoChannel, DataImport, QualityControl, Preprocessing
Depends	methods, Biobase, RColorBrewer, limma, Matrix, grid
Imports	genefilter, limma, vsn
Suggests	rtracklayer, mclust, topGO
System Requirements
License	Artistic-2.0
URL
Depends On Me	Starr
Imports Me
Suggests Me
Version	1.15.1

Package Downloads

Package Source	Ringo_1.15.1.tar.gz
Windows Binary	Ringo_1.15.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	Ringo_1.15.1.tgz
Package Downloads Report	Download Stats