CoCAS: a ChIP-on-chip analysis suite
| Autor: | Pierre Ferrier, Sébastien Jaeger, Jean Imbert, Touati Benoukraf, Pierre Cauchy, Frederic Koch, Romain Fenouil, Salvatore Spicuglia, Adrien Jeanniard, Jean-Christophe Andrau, Denis Thieffry |
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| Přispěvatelé: | Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Technologies avancées pour le génôme et la clinique (TAGC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU) |
| Jazyk: | angličtina |
| Rok vydání: | 2009 |
| Předmět: |
Statistics and Probability
Chromatin Immunoprecipitation Computer science computer.software_genre Biochemistry Genome 03 medical and health sciences MESH: Software 0302 clinical medicine Molecular Biology 030304 developmental biology Oligonucleotide Array Sequence Analysis MESH: Chromatin Immunoprecipitation 0303 health sciences business.industry Suite Replicate ChIP-on-chip Genome Analysis Computer Science Applications Computational Mathematics Applications Note Computational Theory and Mathematics 030220 oncology & carcinogenesis MESH: Oligonucleotide Array Sequence Analysis [SDV.IMM]Life Sciences [q-bio]/Immunology Data mining DNA microarray business Chromatin immunoprecipitation computer Computer hardware Software |
| Zdroj: | Bioinformatics Bioinformatics, 2009, 25 (7), pp.954-5. ⟨10.1093/bioinformatics/btp075⟩ Bioinformatics, Oxford University Press (OUP), 2009, 25 (7), pp.954-5. ⟨10.1093/bioinformatics/btp075⟩ |
| ISSN: | 1367-4803 1367-4811 |
| Popis: | 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. Contact: ferrier@ciml.univ-mrs.fr; andrau@ciml.univ-mrs.fr; spicuglia@ciml.univ-mrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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