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Ringo

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A package that facilitates the analysis of ChIP-chip experiments by providing functionality for data import, quality assessment, normalization and visualization of the data, and the detection of ChIP-enriched genomic regions. Ringo makes the construction of programmed analysis workflows easier, offers benefits in scalability, reproducibility and methodical scope of the analyses and opens up a broad selection of follow-up statistical and bioinformatics methods. Its functionality covers the complete primary analysis for ChIP-chip tiling microarrays, especially those from the company NimbleGen. The package's close integration with other Bioconductor packages opens up a multitude of subsequent analysis approaches.

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Ringo classification

Ringo specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
1.36.0
Requirements:
methods, Biobase, RColorBrewer, limma, Matrix, grid, lattice

Ringo distribution

versioning

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No versioning.

Ringo support

Documentation

Credits

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Publications

Institution(s)

EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Funding source(s)

This work was supported by the European Union (FP6 HeartRepair 018630).

Link to literature

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