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annotatr: Associating genomic regions with genomic annotations

Raymond G. Cavalcante, Maureen A. Sartor
doi: https://doi.org/10.1101/039685
Raymond G. Cavalcante
1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109;
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Maureen A. Sartor
1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109;
2Department of Biostatistics, University of Michigan, Ann Arbor, MI
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Abstract

Motivation Analysis of next-generation sequencing data often results in a list of genomic regions. These may include differentially methylated CpGs/regions, transcription factor binding sites, interacting chromatin regions, or GWAS-associated SNPs, among others. A common analysis step is to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.). Existing tools are limited by requiring an artificial one-to-one region-to-annotation mapping, by a lack of visualization options to clearly and easily summarize annotations, by the time it takes to annotate regions, or by some combination thereof.

Results We have developed the annotatr R package to easily and quickly summarize, and visualize the association of genomic regions with genomic annotations. The annotatr package reports all intersections of regions and annotations, giving a better understanding of the genomic context of the regions. A variety of visualization functions are implemented in annotatr to easily plot numerical or categorical data associated with the regions across the annotations, providing insight into how characteristics of the regions differ across the annotations. We also demonstrate that annotatr is up to 11x faster than the comparable R package, ChIPpeakAnno. Overall, annotatr facilitates easy and fast genomic annotation of genomic regions, enabling a richer biological interpretation of experiments.

Availability http://www.github.com/rcavalcante/annotatr/

Contact rcavalca{at}umich.edu

Supplementary information Supplementary data are available at Bioinformatics online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 15, 2016.
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annotatr: Associating genomic regions with genomic annotations
Raymond G. Cavalcante, Maureen A. Sartor
bioRxiv 039685; doi: https://doi.org/10.1101/039685
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annotatr: Associating genomic regions with genomic annotations
Raymond G. Cavalcante, Maureen A. Sartor
bioRxiv 039685; doi: https://doi.org/10.1101/039685

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