DNABarcodeCompatibility
Bioc currentA Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
The package allows one to obtain optimised combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimiser function to further favor the selection of barcode combinations with least heterogeneity in barcode usage.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
157 7 exported
Complexity
2.5 avg / 21 max
Call network
157 nodes / 95 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
4,605
Files
53
Compiled share
39%
Has compiled src
Yes
Language breakdown
API
Exported functions
7
Internal functions
67
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
15
First release
2019-06-20
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
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 20%
Datasets
| Name | Class | Rows × Cols | Also in |
|---|---|---|---|
| IlluminaIndexes | data.frame | 48 × 4 | No other package |
| IlluminaIndexesRaw | data.frame | 48 × 2 | No other package |
Topics
People
- Céline Trébeau maintainer
- Jacques Boutet de Monvel author
- Raphaël Etournay author
- Fabienne Wong Jun Tai contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("DNABarcodeCompatibility")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 v2026-08-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.