svaRetro
Bioc currentRetrotransposed transcript detection from structural variants
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
12 1 exported
Complexity
2.6 avg / 9 max
Call network
12 nodes / 9 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
877
Files
31
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
9
Testing
Has tests
Yes
Test-to-code ratio
0.06
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
4.0
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 7 (3 internal)includes a package overview page
- Examples that run
- 100%1 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- svaRetro Package HTML
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/papenfusslab/svaretro on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| gene_symbol | data.frame | 82,960 × 2 | No other package |
Topics
People
- Ruining Dong author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("svaRetro")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.