genomation
Bioc currentSummary, annotation and visualization of genomic data
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
95 22 exported
Complexity
5.4 avg / 61 max
Call network
95 nodes / 56 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
12,013
Files
169
Compiled share
5.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
49
Internal functions
17
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
39.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.0.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
23
First release
2015-12-22
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
16
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 92 (33 internal)
- Examples that run
- 100%37 run in a plain check
- Exported functions with examples
- 57%
- Documented parameters
- 98%
- Return-value docs
- 57%
- Help pages citing references
- 0%
- genomation HTML
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/bimsbbioinfo/genomation on 2026-10-22.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| EnhancersEncode.txt | data.frame | 5 × 9 | No other package |
| cage | – | – | – |
| cpgi | – | – | – |
| genes | – | – | – |
| promoters | – | – | – |
Topics
Depended on by (5)
Bioconductor (5)
Suggested by (1)
People (from the free-text Author field)
- Altuna Akalin author maintainer
- Vedran Franke author maintainer
- Katarzyna Wreczycka author
- Alexander Gosdschan contributor
- Liz Ing-Simmons contributor
- Bozena Mika-Gospodorz contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("genomation")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btu775.
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.