openPrimeR
Bioc currentMultiplex PCR Primer Design and Analysis
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the 'openPrimeRui' package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
377 34 exported
Complexity
5.8 avg / 65 max
Call network
377 nodes / 578 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
35,819
Files
894
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
47
Internal functions
343
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
12.5%
Unsafe pattern score
12
Dep constraint coverage
96.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
5 externalMAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3)
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2018-03-22
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
6
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 359 (347 internal)includes a package overview page
- Examples that run
- 90%18 run in a plain check · 2 never run
- Exported functions with examples
- 100%
- Documented parameters
- 95%
- Return-value docs
- 100%
- Help pages citing references
- 3%
- openPrimeR HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| feature.matrix | data.frame | 908 × 32 | No other package |
| primer.data | list | 31 elements | No other package |
| primer.df | Primers | 151 elements | No other package |
| ref.data | data.frame | 940 × 3 | No other package |
| settings | – | – | – |
| template.data | list | 31 elements | No other package |
| template.df | Templates | 35 elements | No other package |
| tiller.primer.df | Primers | 151 elements | No other package |
| tiller.settings | – | – | – |
| tiller.template.df | Templates | 35 elements | No other package |
6 internal objects are bundled for the package's own use and not listed here.
Topics
Depended on by (1)
Bioconductor (1)
People
- Matthias Döring author maintainer
- Nico Pfeifer author
Cite
Cite this package
Run in R for the authors' entry:
citation("openPrimeR")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.