supersigs
Bioc currentSupervised mutational signatures
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
34 6 exported
Complexity
2.6 avg / 6 max
Call network
34 nodes / 26 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
2,096
Files
44
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
28
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
3
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
4.1
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-05-19
Latest release
2026-04-28
Avg cadence
182 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
- 9
- Examples that run
- 100%6 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Using supersigs HTML
Repository practices
4 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/tomasettilab/supersigs on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| example_dt | data.frame | 25 × 6 | No other package |
| supersig_ls | list | 67 elements | No other package |
12 internal objects are bundled for the package's own use and not listed here.
Topics
People
- Albert Kuo author maintainer
- Bahman Afsari author
- Cristian Tomasetti author
- Yifan Zhang author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("supersigs")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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.