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annotatr: genomic regions in context.

Raymond G Cavalcante¹, Maureen A Sartor^1,2

¹Department of Computational Medicine and Bioinformatics.

Bioinformatics (Oxford, England)

|April 4, 2017

Summary

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The annotatr R package quickly annotates genomic regions, providing comprehensive insights into their biological context. It offers faster analysis and improved visualization compared to existing tools.

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Next-generation sequencing data analysis generates lists of genomic regions requiring annotation.
Existing annotation tools have limitations in annotation sources, flexibility, speed, and visualization.
Accurate annotation is crucial for understanding the biological significance of genomic regions.

Purpose of the Study:

To develop a flexible and fast R package for summarizing and visualizing genomic region annotations.
To overcome limitations of existing tools by providing comprehensive annotation and visualization capabilities.
To enable richer biological interpretation of genomic data.

Main Methods:

Developed the annotatr Bioconductor package.
Implemented functions to report all intersections between genomic regions and annotations.

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Integrated diverse graphics functions for plotting data across annotations and intersections.

Main Results:

The annotatr package provides comprehensive annotation by reporting all region-annotation intersections.
It offers versatile plotting functions to visualize data associated with genomic regions across annotations.
annotatr is up to 27 times faster than comparable R packages, enhancing analysis efficiency.

Conclusions:

annotatr enables a more thorough understanding of the genomic context of analyzed regions.
The package facilitates richer biological interpretation of experimental data through enhanced visualization.
annotatr represents a significant improvement in speed and functionality for genomic region annotation.