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

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

Author information

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

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