ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2

Emil K Gustavsson; David Zhang; Regina H Reynolds; Sonia Garcia-Ruiz; Mina Ryten

doi:10.1093/bioinformatics/btac409

ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2

Bioinformatics. 2022 Aug 2;38(15):3844-3846. doi: 10.1093/bioinformatics/btac409.

Authors

Emil K Gustavsson^{1

2}, David Zhang^{1

2}, Regina H Reynolds^{1

2}, Sonia Garcia-Ruiz^{1

2

3}, Mina Ryten^{1

2

3}

Affiliations

¹ Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.
² Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
³ NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK.

Abstract

Motivation: The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.

Availability and implementation: ggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT licence. Further documentation is available at https://dzhang32.github.io/ggtranscript/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Protein Isoforms / genetics
Sequence Analysis, DNA / methods
Software*

Substances

Protein Isoforms

Abstract

Publication types

MeSH terms

Substances

Grants and funding