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 a lack of annotation sources and flexible options, 
the time it takes to annotate regions, an artificial one-to-one 
region-to-annotation mapping, a lack of visualization options to easily 
summarize data, or some combination thereof.
RESULTS: We developed the annotatr Bioconductor package to flexibly and quickly 
summarize and plot annotations of genomic regions. The annotatr package reports 
all intersections of regions and annotations, giving a better understanding of 
the genomic context of the regions. A variety of graphics functions are 
implemented to easily plot numerical or categorical data associated with the 
regions across the annotations, and across annotation intersections, providing 
insight into how characteristics of the regions differ across the annotations. 
We demonstrate that annotatr is up to 27× faster than comparable R packages. 
Overall, annotatr enables a richer biological interpretation of experiments.
AVAILABILITY AND IMPLEMENTATION: http://bioconductor.org/packages/annotatr/ and 
https://github.com/rcavalcante/annotatr.
CONTACT: rcavalca@umich.edu.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.