MutSeqR: an open source R package for standardized analysis of error-corrected next-generation sequencing data in genetic toxicology.

ABSTRACT:

Motivation

Error-corrected next-generation sequencing (ECS) methods are increasingly used to assess mutagenicity and other genetic toxicology endpoints. The lack of open and standardized bioinformatic workflows and tools poses challenges to data reproducibility, comparability, and consistency in interpretation for its application in genetic toxicity assessment.

Results

We present MutSeqR, an open source R package to analyse ECS mutation data for genetic toxicology studies. MutSeqR offers practical variant filtering, comparative analysis of mutation frequency between experimental conditions, dose-response assessment via benchmark dose calculations, mutation spectrum analysis, and clonality analyses. We demonstrate MutSeqR's application using published datasets on mice treated

SUBMITTER: Dodge AE 

PROVIDER: S-EPMC12645840 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature