SomaticSignatures
Bioc currentSomatic Signatures
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
50 32 exported
Complexity
1.7 avg / 8 max
Call network
50 nodes / 30 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
5,544
Files
60
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
32
Internal functions
18
Testing
Has tests
Yes
Test-to-code ratio
0.32
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.1.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-05-11
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 21includes a package overview page
- Examples that run
- 100%15 run in a plain check
- Exported functions with examples
- 73%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 19%
- SomaticSignatures HTML
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/juliangehring/somaticsignatures on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| k3we | table | 64 | No other package |
| k3wg | array | 64 | No other package |
| sca_mm | matrix | 96 × 8 | No other package |
| sca_motifs_tiny | – | – | – |
| signatures21 | matrix | 96 × 27 | No other package |
| sigs_nmf | – | – | – |
| sigs_pca | – | – | – |
Topics
Depended on by (2)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("SomaticSignatures")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btv408.
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.