CoCAS: a ChIP-on-chip analysis suite
corelboy 添加于 2009-10-11 19:53
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作 者
Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau J-C, Spicuglia S, Ferrier P 摘 要
MOTIVATION: High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by this approach, we have developed ChIP-on-chip Analysis Suite (CoCAS), a standalone software suite which implements optimized ChIP-on-chip data normalization, improved peak detection, as well as quality control reports. Our software allows dye swap, replicate correlation and connects easily with genome browsers and other peak detection algorithms. CoCAS can readily be used on the latest generation of Agilent high-density arrays. Also, the implemented peak detection methods are suitable for other datasets, including ChIP-Seq output. AVAILABILITY: The software is available for download along with a sample dataset at http://www.ciml.univ-mrs.fr/software/ferrier.htm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.-
详细资料
- 关键词: Chromatin Immunoprecipitation/*methods; Oligonucleotide Array Sequence Analysis/*methods; *Software
- 文献种类: Journal Article
- 期刊名称: Bioinformatics (Oxford, England)
- 期刊缩写: Bioinformatics
- 期卷页: 2009年 第25卷 第7期 954-955页
- 地址: Centre d'Immunologie de Marseille-Luminy, CNRS, UMR6102, Inserm, U631, Universite de la Mediterranee and Inserm, U928, TAGC, Marseille, France
- ISBN: 1460-2059
- 备注:PMID:19193731
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学科领域 生物医药 » 基础医学
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