rhinotypeR
Bioc currentRhinovirus genotyping
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
"rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, "rhinotypeR" supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
17 11 exported
Complexity
4.4 avg / 17 max
Call network
17 nodes / 10 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
3,939
Files
59
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
6
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.49
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-10-29
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
- Help pages
- 15 (1 internal)includes a package overview page
- Examples that run
- 93%13 run in a plain check (4 of them under a condition) · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 90%
- Return-value docs
- 100%
- Help pages citing references
- 20%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/omicscodeathon/rhinotyper on 2026-10-25.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| prototypes | data.frame | 169 × 3 | No other package |
| rhinovirusPrototypesVP4 | – | – | – |
| rhinovirusVP4 | – | – | – |
Topics
People
- Martha Luka author maintainer
- Olaitan Awe author
- Winfred Gatua author
- Ruth Nanjala author
- Wafaa M. Rashed author
Cite
Cite this package
Run in R for the authors' entry:
citation("rhinotypeR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41598-026-37050-8.
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.