GenomAutomorphism
Bioc currentCompute the automorphisms between DNA's Abelian group representations
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 17 exported
Complexity
5.1 avg / 12 max
Call network
49 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
16,271
Files
202
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
77
Internal functions
32
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.03
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
4.6.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2023-02-24
Latest release
2026-07-31
Avg cadence
189 days
Cold removal rate
–
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 83 (31 internal)includes a package overview page
- Examples that run
- 100%61 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 68%
- Return-value docs
- 100%
- Help pages citing references
- 18%
- Fix a bug in the internal function 'weighted_manhattan' (used by 'codon_dist', 'codon_dist_matrix', and 'aminoacid_dist') where, for \eqn{group = "Z4"}, the second coordinate weight ('w[2]') was silently omitted and 'w[3]' was applied twice instead, contradicting the documented weighted Manhattan distance formula. This changes the numeric distances returned for \emph{group = "Z4"} (the default). The bundled 'cdm_z64' dataset was regenerated accordingly.
- Documentation updated
From NEWS.md in the release
Repository practices
Checks run against github.com/genomaths/genomautomorphism on 2026-10-25.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| aaindex1 | list | 2 elements | No other package |
| aaindex2 | list | 2 elements | No other package |
| aaindex3 | list | 2 elements | No other package |
| aln | – | – | – |
| autby_coef | – | – | – |
| autm | – | – | – |
| autm_3d | – | – | – |
| autm_z125 | – | – | – |
| brca1_aln | – | – | – |
| brca1_aln2 | – | – | – |
| brca1_autm | – | – | – |
| brca1_autm2 | – | – | – |
| cdm_z64 | list | 24 elements | No other package |
| covid_aln | – | – | – |
| covid_autm | – | – | – |
| cyc_aln | – | – | – |
| cyc_autm | – | – | – |
| dna_phyche | data.frame | 4 × 4 | No other package |
Topics
People
- Robersy Sanchez author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("GenomAutomorphism")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 v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.