ArticleBioinformatics advances2025
MutSeqR: an open source R package for standardized analysis of error-corrected next-generation sequencing data in genetic toxicology.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
2 citing papers in PubMed.
- Differential Mutagenic Response of Rat Liver and Lung to Nicotine-Derived Nitrosamine Ketone (NNK).Chemical research in toxicology · 2026Article
- Benzo[b]fluoranthene Induces Mutation Accumulation and Cancer-Relevant Mutational Signatures in Mouse Lung Alongside Steady State Levels of Chromosome Damage in Blood.Environmental and molecular mutagenesis · 2026Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
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 with benzo[a]pyrene or benzo[b]fluoranthene, analysed using Duplex Sequencing and SMM-seq, respectively. MutSeqR's flexible functions enable reproducible analyses across ECS platforms, facilitating research and regulatory applications in mutagenicity testing. Availability and implementation: MutSeqR is freely available under an open source license at https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqR. Implemented in R (version 3.4.0 or greater), it supports all major operating systems. Sequencing data for Project 1 has been deposited in the Sequence Read Archive under accession number PRJNA803048. Variant call files for Project 2 are available on Mendeley Data (doi: 10.17632/65dnysxym8.1).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.