title: DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies.
abstract: The genome-wide study of epigenetic states requires the integrative analysis of histone modification ChIP-seq data. Here, we introduce an easy-to-use analytic framework to compare profiles of enrichment in histone modifications around classes of genomic elements, e.g. transcription start sites (TSS). Our framework is available via the user-friendly R/Bioconductor package DChIPRep. DChIPRep uses biological replicate information as well as chromatin Input data to allow for a rigorous assessment of differential enrichment. DChIPRep is available for download through the Bioconductor project at http://bioconductor.org/packages/DChIPRep. Contact. DChIPRep@gmail.com.
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Oncology iMed, CRUK-Cambridge Institute, Astra Zeneca, Cambridge, United Kingdom.
authors.forename: Christophe D
authors.initials: CD
authors.lastname: Chabbert
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States; Department of Genetics, Stanford University School of Medicine, Stanford, California, United States.
authors.forename: Lars M
authors.initials: LM
authors.lastname: Steinmetz
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory , Heidelberg , Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Klaus
keywords: Bioinformatics; ChiP-seq; Chromatin; Computational Biology; Differential enrichment; Genomics; Histone-modifications; Statistics