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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 ... This identification can be improved by accounting for dependencies between adjacent probes on chromosomes and by modeling of biological replicates. ... Acknowledgements This work was funded by MIA, BAP and MICA departments of INRA, and supported by the TAG ANR/Genoplante project. MS was supported by the DAAD PROCOPE (grant 50748812). ...doi:10.1186/1471-2105-14-271 pmid:24015679 pmcid:PMC3846700 fatcat:lml6ul6rm5gmfjofifqubdx674