MutSeqR: an open source R package for standardized analysis of error-corrected next-generation sequencing data in genetic toxicology
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic 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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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it