Genomation: A Toolkit to Summarize, Annotate and Visualize Genomic Intervals

Bioinformatics. 2015 Apr 1;31(7):1127-9. doi: 10.1093/bioinformatics/btu775. Epub 2014 Nov 21.

Abstract

Biological insights can be obtained through computational integration of genomics data sets consisting of diverse types of information. The integration is often hampered by a large variety of existing file formats, often containing similar information, and the necessity to use complicated tools to achieve the desired results. We have built an R package, genomation, to expedite the extraction of biological information from high throughput data. The package works with a variety of genomic interval file types and enables easy summarization and annotation of high throughput data sets with given genomic annotations.

Availability and implementation: The software is currently distributed under MIT artistic license and freely available at http://bioinformatics.mdc-berlin.de/genomation, and through the Bioconductor framework.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • Computer Graphics*
  • Databases, Genetic
  • Exons / genetics*
  • Genome, Human
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Introns / genetics*
  • Molecular Sequence Annotation*
  • Software*