sitadela
Bioc currentAn R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
141 20 exported
Complexity
5.4 avg / 58 max
Call network
141 nodes / 272 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
11,921
Files
39
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
121
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
2
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-10-13
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
- Help pages
- 11
- Examples that run
- 100%11 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/pmoulos/sitadela on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| dasNov3_JH569334 | – | – | – |
| dicLab1_LG3 | – | – | – |
| eboVir3_KM034562v1 | – | – | – |
| gadMor1_HE567025 | – | – | – |
Topics
People
- Panagiotis Moulos author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("sitadela")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.