Ringo

R Investigation of ChIP-chip Oligoarrays

Bioconductor version: Development (3.0)

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 <jtoedling at yahoo.de>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("Ringo")

Documentation

PDF R Script R Investigation of NimbleGen Oligoarrays
PDF   Reference Manual

Details

biocViews DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.29.0
In Bioconductor since BioC 2.0 (R-2.5)
License Artistic-2.0
Depends methods, Biobase(>= 1.14.1), RColorBrewer, limma, Matrix, grid, lattice
Imports BiocGenerics(>= 0.1.11), genefilter, limma, vsn, stats4
Suggests rtracklayer(>= 1.3.1), mclust, topGO(>= 1.15.0)
System Requirements
URL
Depends On Me ccTutorial, SimBindProfiles, Starr
Imports Me Repitools
Suggests Me

Package Downloads

Package Source Ringo_1.29.0.tar.gz
Windows Binary Ringo_1.29.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Ringo_1.29.0.tgz
Mac OS X 10.9 (Mavericks)
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