Ringo

R Investigation of ChIP-chip Oligoarrays

Bioconductor version: 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 <joern.toedling at curie.fr>

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 Microarray, TwoChannel, DataImport, QualityControl, Preprocessing
Depends methods, Biobase(>= 1.14.1), RColorBrewer, limma, Matrix, grid
Imports genefilter, limma, vsn
Suggests rtracklayer(>= 1.3.1), mclust, topGO(>= 1.15.0)
System Requirements
License Artistic-2.0
URL
Depends On Me Starr
Imports Me
Suggests Me
Version 1.16.0
Since Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source Ringo_1.16.0.tar.gz
Windows Binary Ringo_1.16.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary Ringo_1.16.0.tgz
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