ggmsa
Bioc currentPlot Multiple Sequence Alignment using 'ggplot2'
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
82 30 exported
Complexity
2.4 avg / 18 max
Call network
82 nodes / 62 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
4,728
Files
104
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
30
Internal functions
52
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
0%
Unsafe pattern score
0
Dep constraint coverage
11.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 42
- Examples that run
- 100%20 run in a plain check
- Exported functions with examples
- 60%
- Documented parameters
- 99%
- Return-value docs
- 97%
- Help pages citing references
- 0%
- ggmsa HTML
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/yulab-smu/ggmsa on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| RF03120_SS | data.frame | 1 × 1 | 2 packages |
5 internal objects are bundled for the package's own use and not listed here.
Topics
Depended on by (1)
CRAN (1)
People
- Guangchuang Yu author maintainer thesis advisor
- Huina Huang contributor
- Shuangbin Xu contributor
- Lang Zhou author
Cite
Cite this package
Run in R for the authors' entry:
citation("ggmsa")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bib/bbac222.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.