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

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)...

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Detalles Bibliográficos
Autores principales: Chabbert, Christophe D., Steinmetz, Lars M., Klaus, Bernd
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2016
Materias:
Bioinformatics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860309/
https://www.ncbi.nlm.nih.gov/pubmed/27168989
http://dx.doi.org/10.7717/peerj.1981
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author Chabbert, Christophe D.
Steinmetz, Lars M.
Klaus, Bernd
author_facet Chabbert, Christophe D.
Steinmetz, Lars M.
Klaus, Bernd
author_sort Chabbert, Christophe D.
collection PubMed
description 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.
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spelling pubmed-48603092016-05-10 DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies Chabbert, Christophe D. Steinmetz, Lars M. Klaus, Bernd PeerJ Bioinformatics 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. PeerJ Inc. 2016-04-26 /pmc/articles/PMC4860309/ /pubmed/27168989 http://dx.doi.org/10.7717/peerj.1981 Text en © 2016 Chabbert et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , 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) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Chabbert, Christophe D.
Steinmetz, Lars M.
Klaus, Bernd
DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
title DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
title_full DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
title_fullStr DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
title_full_unstemmed DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
title_short DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
title_sort dchiprep, an r/bioconductor package for differential enrichment analysis in chromatin studies
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860309/
https://www.ncbi.nlm.nih.gov/pubmed/27168989
http://dx.doi.org/10.7717/peerj.1981
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