mutscan
Bioc currentPreprocessing and Analysis of Deep Mutational Scanning Data
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
Provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
100 18 exported
Complexity
8.4 avg / 125 max
Call network
100 nodes / 100 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
15,861
Files
96
Compiled share
22.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
18
Internal functions
22
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
1.99
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
7.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
1 externalGNU make
C++ standard
C++17
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 16
- Examples that run
- 100%16 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 88%
- Return-value docs
- 100%
- Help pages citing references
- 6%
- mutscan HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/fmicompbio/mutscan on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-08-03 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| GSE102901_cis_se | – | – | – |
| multipleVariableRegions_truth | list | 5 elements | No other package |
Topics
People
- Charlotte Soneson author maintainer
- Friedrich Miescher Institute for Biomedical Research copyright holder
- Michael Stadler author
Cite
Cite this package
Run in R for the authors' entry:
citation("mutscan")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-023-02967-0.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.