annmap
Bioc currentGenome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Release Lineage
Entered 2.11 · Oct 3, 2012
Current · Requires R 4.6
Description
annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
217 0 exported
Complexity
4 avg / 70 max
Call network
217 nodes / 441 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
5,850
Files
63
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
155
Internal functions
61
Testing
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
0
Dep constraint coverage
8.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.15.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
28
First release
2012-10-01
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
–
Dep drift
0
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
- 100%11 run in a plain check (11 of them under a condition)
- Exported functions with examples
- 85%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 7%
Repository practices
Checks run against github.com/cruk-mi/annmap on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("annmap")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.