{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T17:13:13Z","timestamp":1764349993439},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2797,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: The software is available for download along with a sample dataset at http:\/\/www.ciml.univ-mrs.fr\/software\/ferrier.htm.<\/jats:p>\n               <jats:p>Contact: \u00a0ferrier@ciml.univ-mrs.fr; andrau@ciml.univ-mrs.fr; spicuglia@ciml.univ-mrs.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp075","type":"journal-article","created":{"date-parts":[[2009,2,5]],"date-time":"2009-02-05T01:56:04Z","timestamp":1233798964000},"page":"954-955","source":"Crossref","is-referenced-by-count":19,"title":["CoCAS: a ChIP-on-chip analysis suite"],"prefix":"10.1093","volume":"25","author":[{"given":"Touati","family":"Benoukraf","sequence":"first","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"Pierre","family":"Cauchy","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"},{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"Romain","family":"Fenouil","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"Adrien","family":"Jeanniard","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"Frederic","family":"Koch","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"S\u00e9bastien","family":"Jaeger","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"Denis","family":"Thieffry","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"},{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"Jean","family":"Imbert","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"},{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"Jean-Christophe","family":"Andrau","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de Marseille-Luminy, 2CNRS, UMR6102, 3Inserm, U631, 4Universit\u00e9 de la M\u00e9diterran\u00e9e and 5Inserm, U928, TAGC, Marseille, France"}]},{"given":"Salvatore","family":"Spicuglia","sequence":"additional","affiliation":[{"name":"1\u20134 \u00a01Centre d'Immunologie de 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