Visual integration of GWAS and differential expression results with the hidecan R package

Genes

Presentation of the hidecan R package for generating visualisations combining GWAS and differential expression analyses results, as well as manually curated candidate genes.
r-package
multi-omics
Author

Olivia Angelin-Bonnet, Matthieu Vignes, Patrick J. Biggs, Samantha Baldwin, Susan Thomson

Published

September 25, 2024

Abstract

Background/Objectives: We present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature. This tool is applicable to all ploidy levels; we notably provide functionalities to facilitate the visualisation of GWAS results obtained for autotetraploid organisms with the GWASpoly package.

Results: We illustrate the capabilities of hidecan with examples from two autotetraploid potato datasets.

Conclusions: The hidecan package is implemented in R and is publicly available on the CRAN repository and on GitHub. A description of the package, as well as a detailed tutorial, is made available alongside the package. It is also part of the VIEWpoly tool for the visualisation and exploration of results from polyploids computational tools.

Cite us

Angelin-Bonnet, O., Vignes, M., Biggs, P.J., Baldwin, S. and Thomson, S., 2024. Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package. Genes, 15(10), p.1244.

Or with bibtex:

@article{angelin2024visual,
  title={Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package},
  author={Angelin-Bonnet, Olivia and Vignes, Matthieu and Biggs, Patrick J and Baldwin, Samantha and Thomson, Susan},
  journal={Genes},
  volume={15},
  number={10},
  pages={1244},
  year={2024},
  publisher={MDPI}
}