seqRdna

seqRdna is an R package developed by MuscleOmicsLab to facilitate the analysis of rDNA copy number and DNA methylation using high-throughput sequencing data.

The package provides a collection of functions for extracting rDNA-specific data, estimating copy number, calculating methylation levels and identifying differential methylation between experimental conditions.

Installation

Install seqRdna from Bioconductor using BiocManager:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("seqRdna")

# Load the package
library(seqRdna)

Link to Useful Resources

Manuscript highlighting examples of seqRdna

Vaughan, D., Wood, N. and Seaborne, R.A., 2026. The ribosomal DNA landscape of 
mammalian muscle during acute and chronic physiological stress. bioRxiv, 
pp.2026-08.

Bibtex for latex users:

@article{vaughan2026ribosomal,
  title={The ribosomal DNA landscape of mammalian muscle during acute and 
  chronic physiological stress},
  author={Vaughan, Daniel and Wood, Nathanael and Seaborne, Robert AE},
  journal={bioRxiv},
  pages={2026--08},
  year={2026},
  publisher={Cold Spring Harbor Laboratory}
}

Data used in the user guide and vignette:

Oyabu M, Ohira Y, Fujita M, Yoshioka K et al. Dnmt3a overexpression disrupts 
skeletal muscle homeostasis, promotes an aging-like phenotype, and reduces 
metabolic elasticity. iScience 2025 Apr 18;28(4):112144. 

GEO

Contributing

We welcome contributions in any form: suggestions, issues, bugfixes. Pull requests should be made to the development branch.