gDNAx
Bioc currentDiagnostics for assessing genomic DNA contamination in RNA-seq data
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 10 exported
Complexity
5.8 avg / 21 max
Call network
49 nodes / 54 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
4,304
Files
28
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
39
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2024-03-15
Latest release
2026-04-28
Avg cadence
150 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
- 7 (1 internal)includes a package overview page
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 92%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- The gDNAx package HTML
USER VISIBLE CHANGES
- Changed default useRMSK=TRUE to useRMSK=FALSE in gDNAdx().
BUG FIXES
- Fix in the calculations of the strandedness() function, and its corresponding unit tests.
From NEWS in the release
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/functionalgenomics/gdnax on 2026-10-18.
The R CMD check workflow runs on Linux
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| cached_gDNAtx_fstats | data.frame | 9 × 7 | No other package |
| gdnax | – | – | – |
Topics
People
- Robert Castelo author maintainer
- Beatriz Calvo-Serra author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("gDNAx")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 v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.