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m6ASeqTools: An R toolkit for post-processing m6A sites detected by m6Anet.
Hanna Lee1, Denalda Gashi1, Syeda Maheen Batool1
1Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Biorxiv : the Preprint Server for Biology
|September 2, 2025
Summary
m6ASeqTools is an R package that simplifies the analysis of N6-methyladenosine (m6A) RNA modifications. It helps researchers understand how m6A patterns relate to gene expression and transcriptional regulation.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Biology
Background:
- N6-methyladenosine (m6A) is a crucial epitranscriptomic modification impacting RNA metabolism and gene expression.
- Accurate post-processing and interpretation of m6A data are essential for understanding its regulatory roles.
- Existing tools may lack comprehensive features for analyzing site-level m6A predictions and integrating them with other omics data.
Purpose of the Study:
- To introduce m6ASeqTools, an R package for streamlined post-processing and interpretation of m6A predictions.
- To provide tools for summarizing m6A distribution across various genomic and transcriptomic features.
- To enable the integration of m6A data with differential gene expression analysis for deeper biological insights.
Main Methods:
- Development of an R package, m6ASeqTools, utilizing R/Bioconductor infrastructure.
- Implementation of functions for descriptive summaries of m6A distribution (transcripts, genes, biotypes, regions).
- Integration of differential gene expression data with m6A modification ratios for comparative analysis.
Main Results:
- m6ASeqTools offers comprehensive summaries of m6A distribution across multiple biological levels.
- The package facilitates condition comparisons using a weighted modification ratio.
- Integration with differential gene expression data reveals links between m6A patterns and transcriptional regulation.
Conclusions:
- m6ASeqTools provides a valuable resource for researchers studying m6A RNA modifications.
- The package enhances the interpretation of m6A-seq data by linking methylation patterns with gene expression.
- Biotype-specific and region-specific analyses offered by m6ASeqTools yield novel insights into epitranscriptomic regulation.
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