Ringo

R Investigation of ChIP-chip Oligoarrays

Bioconductor version: 2.9

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 <j.toedling at imb-mainz.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")

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