title: CoCAS: a ChIP-on-chip analysis suite.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The software is available for download along with a sample dataset at http://www.ciml.univ-mrs.fr/software/ferrier.htm.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Centre d'Immunologie de Marseille-Luminy, CNRS, UMR6102, Inserm, U631, Université de la Méditerranée and Inserm, U928, TAGC, Marseille, France.
authors.forename: Touati
authors.initials: T
authors.lastname: Benoukraf
authors.forename: Pierre
authors.initials: P
authors.lastname: Cauchy
authors.forename: Romain
authors.initials: R
authors.lastname: Fenouil
authors.forename: Adrien
authors.initials: A
authors.lastname: Jeanniard
authors.forename: Frederic
authors.initials: F
authors.lastname: Koch
authors.forename: Sébastien
authors.initials: S
authors.lastname: Jaeger
authors.forename: Denis
authors.initials: D
authors.lastname: Thieffry
authors.forename: Jean
authors.initials: J
authors.lastname: Imbert
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Andrau
authors.forename: Salvatore
authors.initials: S
authors.lastname: Spicuglia
authors.forename: Pierre
authors.initials: P
authors.lastname: Ferrier
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software