MutSeqR
Bioc currentAnalysis of Error-Corrected Sequencing Data for Mutation Detection
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
Standard methods for analysis of mutation data following error- corrected sequencing (ECS) for the purpose of mutagencity assessment. Functions include importing the mutation lists provided by a variant caller, and a set of analytical tools for statistical testing and visualization of mutation data; comparison to COSMIC and/or germline signatures; etc.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
132 34 exported
Complexity
30.1 avg / 387 max
Call network
132 nodes / 222 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
33,433
Files
151
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
41
Internal functions
98
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
3
Docs
Roxygen coverage
97.6%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
10%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
Python via reticulate
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 64 (3 internal)
- Examples that run
- 95%37 run in a plain check (1 of them under a condition) · 1 only when donttest examples are enabled (R CMD check --as-cran) · 1 hold no code
- Exported functions with examples
- 95%
- Documented parameters
- 100%
- Return-value docs
- 85%
- Help pages citing references
- 0%
Repository practices
7 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/ehsrb-bsrse-bioinformatics/mutseqr on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-10-09 · The repository has a site deploy workflow
pkgdown site last built 2026-10-09
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ASCII_art_MutSeqR | – | – | – |
| filtered_simple_mutation_data | data.frame | 35 × 33 | No other package |
| human_mutagenesis_panel_hg38 | data.frame | 20 × 9 | No other package |
| mf_data_6 | tibble | 48 × 11 | No other package |
| mf_data_6_sample | tibble | 264 × 11 | No other package |
| mf_data_96 | tibble | 384 × 11 | No other package |
| mf_data_96_sample | tibble | 2,304 × 13 | No other package |
| mf_data_global | data.frame | 24 × 8 | No other package |
| mf_model_global | list | 10 elements | No other package |
| mouse_mutagenesis_panel_mm10 | data.frame | 20 × 8 | No other package |
| rat_mutagenesis_panel_rn6 | data.frame | 20 × 7 | No other package |
| simple_mut_import | data.frame | 36 × 9 | No other package |
| simple_mutation_data | tibble | 36 × 30 | No other package |
| variants_subset_d50_chr1 | tibble | 189 × 44 | No other package |
Topics
People
- Matthew J. Meier author maintainer
- Burroughs Wellcome Fund funder
-
Canada Research Chairs Program
funder
CRC-2020-00060
- Health Canada's Genomics Research and Development Initiative funder
- Christopher Bradley author
- Annette E. Dodge author
- Elena Esina author
- Danielle P.M. LeBlanc author
- Francesco Marchetti author
- Alexander Y. Maslov author
- Geronimo Matteo contributor
- Jesse J. Salk author
- David M. Schuster author
- Clint C. Valentine author
- Andrew Williams author
- Carole L. Yauk author
Cite
Cite this package
Run in R for the authors' entry:
citation("MutSeqR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioadv/vbaf265.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.