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	Microarray , TwoChannel , DataImport , QualityControl , Preprocessing
Depends	graphics, methods, Biobase, genefilter, geneplotter, limma, vsn, RColorBrewer, SparseM
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License	Artistic License 2.0
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