atena
Bioc currentAnalysis of Transposable Elements
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
121 15 exported
Complexity
3.9 avg / 22 max
Call network
121 nodes / 141 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
8,204
Files
46
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
106
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
4.3.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-12-16
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 14includes a package overview page
- Examples that run
- 92%12 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 43%
BUG FIXES
- Fix in OneCodeToFindThemAll() when the 'dictionary' argument is not NULL.
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/rcastelo/atena on 2026-10-21.
The R CMD check workflow runs on Linux
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Top28TEs | – | – | – |
| Top50genes | – | – | – |
| rmskatLTRrlen80flenpartoth | – | – | – |
Topics
People
- Robert Castelo author maintainer
- Beatriz Calvo-Serra author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("atena")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.