Ringo

R Investigation of NimbleGen Oligoarrays

The package Ringo simplifies the analysis of two-color oligonucleotide microarrays from NimbleGen, which for example can be used in ChIP-chip projects. The package employs functions from various other packages of the Bioconductor project and provides additional NimbleGen-specific and ChIP-chip-specific functionalities. Its mainly covered subjects are data read-in, quality control, visualisation and identification of genomic regions showing enrichment in ChIP-chip. Please take note that Ringo is geared towards two-color NimbleGen microarrays. For single-channel NimbleGen arrays, we recommend the package 'oligo'.

Author Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber
Maintainer J. Toedling

To install this package, start R and enter:

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

Vignettes (Documentation)

Package Downloads

Ringo.pdf
Rplots.pdf
Source Ringo_1.4.0.tar.gz
Windows binary Ringo_1.4.0.zip
OS X binary Ringo_1.4.0.tgz

Details

biocViews
Depends graphics, methods, Biobase, genefilter, geneplotter, limma, vsn, RColorBrewer, SparseM
Suggests
Imports
SystemRequirements
License Artistic License 2.0
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