PT  - JOURNAL ARTICLE
AU  - Raymond G. Cavalcante
AU  - Maureen A. Sartor
TI  - annotatr: Associating genomic regions with genomic annotations
AID  - 10.1101/039685
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 039685
4099  - http://biorxiv.org/content/early/2016/02/15/039685.short
4100  - http://biorxiv.org/content/early/2016/02/15/039685.full
AB  - 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.eduSupplementary information Supplementary data are available at Bioinformatics online.