Structstrings
Bioc currentImplementation of the dot bracket annotations with Biostrings
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
88 19 exported
Complexity
2.8 avg / 16 max
Call network
88 nodes / 74 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
4,215
Files
49
Compiled share
13.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
30
Internal functions
51
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
30%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-06-11
Latest release
2026-04-28
Avg cadence
182 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
- Help pages
- 11 (1 internal)includes a package overview page
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 78%
- Return-value docs
- 88%
- Help pages citing references
- 9%
- Structstrings HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/felixernst/structstrings on 2026-10-25.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2025-09-23 · The repository has a site deploy workflow
Datasets
Topics
Depended on by (3)
Bioconductor (3)
People
- Felix G.M. Ernst author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("Structstrings")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.