syntenet
Bioc currentInference And Analysis Of Synteny Networks
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
74 29 exported
Complexity
2.8 avg / 8 max
Call network
74 nodes / 64 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
7,128
Files
108
Compiled share
18%
Has compiled src
Yes
Language breakdown
API
Exported functions
29
Internal functions
12
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.27
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
6.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2023-03-14
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- References docs
- 15%
Topics
Depended on by (1)
Bioconductor (1)
People
- FabrÃcio Almeida-Silva author maintainer
- Kristian K Ullrich author
- Yves Van de Peer author
- Tao Zhao author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("syntenet")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.