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Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts

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Item Type:Article
Title:Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts
Creators Name:Toedling, J. and Skylar, O. and Krueger, T. and Fischer, J.J. and Sperling, S. and Huber, W.
Abstract:Background: Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is a high-throughput assay for DNA-protein-binding or post-translational chromatin/histone modifications. However, the raw microarray intensity readings themselves are not immediately useful to researchers, but require a number of bioinformatic analysis steps. Identified enriched regions need to be bioinformatically annotated and compared to related datasets by statistical methods. Results: We present a free, open-source R package Ringo 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. Conclusion: Ringo integrates with other packages of the Bioconductor project, uses common data structures and is accompanied by ample documentation. It facilitates the construction of programmed analysis workflows, offers benefits in scalability, reproducibility and methodical scope of the analyses and opens up a broad selection of follow-up statistical and bioinformatic methods.
Keywords:Algorithms, Chromatin Immunoprecipitation, Chromosome Mapping, Computer-Assisted Image Interpretation, Fluorescence In Situ Hybridization, Multiphoton Fluorescence Microscopy, Oligonucleotide Array Sequence Analysis, Programming Languages, Software
Source:BMC Bioinformatics
Publisher:BioMed Central
Page Range:221
Date:26 June 2007
Official Publication:https://doi.org/10.1186/1471-2105-8-221
PubMed:View item in PubMed

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