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R Investigation of ChIP-chip Oligoarrays

Bioconductor version: Release (3.5)

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>

Citation (from within R, enter citation("Ringo")):


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PDF R Script R Investigation of NimbleGen Oligoarrays
PDF   Reference Manual


biocViews DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.40.0
In Bioconductor since BioC 2.0 (R-2.5) (10.5 years)
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)
Depends On Me ccTutorial, SimBindProfiles, Starr
Imports Me Repitools
Suggests Me
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