DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies

Christophe D Chabbert; Lars M Steinmetz; Bernd Klaus

doi:10.7717/peerj.1981

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies

PeerJ. 2016 Apr 26:4:e1981. doi: 10.7717/peerj.1981. eCollection 2016.

Authors

Christophe D Chabbert¹, Lars M Steinmetz², Bernd Klaus³

Affiliations

¹ Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Oncology iMed, CRUK-Cambridge Institute, Astra Zeneca, Cambridge, United Kingdom.
² 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.
³ Genome Biology Unit, European Molecular Biology Laboratory , Heidelberg , Germany.

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.

Keywords: Bioinformatics; ChiP-seq; Chromatin; Computational Biology; Differential enrichment; Genomics; Histone-modifications; Statistics.

Grants and funding

This work was supported by a PhD fellowship from Boerhinger Ingelheim Fonds (to C.D.C); and the Deutsche Forschungsgemeinschaft (1422/3-1 to L.M.S.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.