title: MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates.
abstract: BACKGROUND
  Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method to identify protein-DNA interactions or chromatin/histone modifications. The robust identification of ChIP-enriched regions is frequently complicated by noisy measurements. This identification can be improved by accounting for dependencies between adjacent probes on chromosomes and by modeling of biological replicates.
  
  
  RESULTS
  MultiChIPmixHMM is a user-friendly R package to analyse ChIP-chip data modeling spatial dependencies between directly adjacent probes on a chromosome and enabling a simultaneous analysis of replicates. It is based on a linear regression mixture model, designed to perform a joint modeling of immunoprecipitated and input measurements.
  
  
  CONCLUSIONS
  We show the utility of MultiChIPmixHMM by analyzing histone modifications of Arabidopsis thaliana. MultiChIPmixHMM is implemented in R and including functions in C, freely available from the CRAN web site: http://cran.r-project.org.
authors.affiliation: INRA, UMR 518 MIA, F-75005 Paris, France. caroline.berard@univ-rouen.fr.
authors.forename: Caroline
authors.initials: C
authors.lastname: Bérard
authors.forename: Michael
authors.initials: M
authors.lastname: Seifert
authors.forename: Tristan
authors.initials: T
authors.lastname: Mary-Huard
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Martin-Magniette
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D006657:Histones / Q000235:genetics; D016014:Linear Models; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics
chemical_list: D006657:Histones; D010940:Plant Proteins