DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
A peer-reviewed article of this Preprint also exists.
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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
Cite this as
2016. DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies. PeerJ PrePrints 4:e1723v2 https://doi.org/10.7287/peerj.preprints.1723v2note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
Supplemental item 2 contained a previous version of ReproduceFiguresDChIPRepPaper.Rmd that does not reproduce the figures. The correct file has been added.
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Supplemental Information
Code and data to reproduce the analysis performed
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Christophe D Chabbert conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Lars M Steinmetz conceived and designed the experiments, reviewed drafts of the paper.
Bernd Klaus conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
Raw data and analysis code to reproduce the paper figures is available as supplemental material.
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.
