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

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1 Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
2 Oncology iMed, CRUK-Cambridge Institute, Astra Zeneca, Cambridge, United Kingdom
3 Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States
4 Department of Genetics, Stanford University School of Medicine, Stanford, California, United States
DOI
10.7287/peerj.preprints.1723v2
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology, Genomics, Statistics
Keywords
Bioinformatics, Computational Biology, Genomics, ChiP–Seq, Chromatin, Histone–Modifications, Differential Enrichment, Statistics
Copyright
© 2016 Chabbert et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Chabbert CD, Steinmetz LM, Klaus B. 2016. DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies. PeerJ PrePrints 4:e1723v2

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 [email protected]

Author Comment

Supplemental item 2 contained a previous version of ReproduceFiguresDChIPRepPaper.Rmd that does not reproduce the figures. The correct file has been added.

Supplemental Information

Package vignette as available from Bioconductor

DOI: 10.7287/peerj.preprints.1723v2/supp-1

Code and data to reproduce the analysis performed

DOI: 10.7287/peerj.preprints.1723v2/supp-2