ModSeqR: an R package for efficient analysis of modified nucleotide data

BMC Genomics 2026 Open access

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Authors: Hailey E. Zimmerman, Jordan L Moore, Ryan H. Miller, Isaac Stirland, Andrew Jenkins, Erin Saito, Tim Jenkins, Jonathon T. Hill
DOI: 10.1186/s12864-026-12655-5
Cited by: 1
References: 17

Abstract

DNA methylation regulates a wide range of biological processes, including gene expression, disease progression, and cell identity. Long-read technologies now enable more comprehensive and accurate methylome analyses than ever before, but they are hindered by the computational resources needed to analyze the massive datasets. Here, we present the CH3 file format, which aids data storage and transfer by reducing file sizes by more than 95%, and the ModSeqR R package, which builds on the CH3 format and a database backend to enable a broad range of epigenetic analyses. Together, these tools enable high-throughput methylation analysis while minimizing computational resource requirements.

Fields of Study & Subjects

Gene expression and cancer classification Genomics and Phylogenetic Studies Single-cell and spatial transcriptomics

Publication details

Journal / source
BMC Genomics
Publisher
Springer Science and Business Media LLC
Volume
27
Issue
1
Publication date
22 February 2026
Language
EN