TY - JOUR
T1 - CoCAS
T2 - A ChIP-on-chip analysis suite
AU - Benoukraf, Touati
AU - Cauchy, Pierre
AU - Fenouil, Romain
AU - Jeanniard, Adrien
AU - Koch, Frederic
AU - Jaeger, Sébastien
AU - Thieffry, Denis
AU - Imbert, Jean
AU - Andrau, Jean Christophe
AU - Spicuglia, Salvatore
AU - Ferrier, Pierre
N1 - Funding Information:
Funding: Inserm, CNRS, Association pour la Recherche sur le Cancer, Institut National du Cancer, Fondation de France, Association Laurette Fugain, Fondation Princesse Grace de Monaco and Commission of the European Communities (to Ferrier laboratory); Inserm, Université de la Méditerranée and Association pour la Recherche sur le Cancer (to Imbert laboratory); Agence Nationale de la Recherche (ANR-06-BYOS-0006 for collaboration between the two groups and to T.B.); fellowship from Institut National du Cancer (to P.C.); Marie Curie Research Training Network (RTN ‘Chromatin Plasticity’) from the Commission of the European Communities (to F.K.).
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=63549142613&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btp075
DO - 10.1093/bioinformatics/btp075
M3 - Article
C2 - 19193731
AN - SCOPUS:63549142613
SN - 1367-4803
VL - 25
SP - 954
EP - 955
JO - Bioinformatics
JF - Bioinformatics
IS - 7
ER -