GenomicAlignments
Bioc currentRepresentation and manipulation of short genomic alignments
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
177 45 exported
Complexity
3.1 avg / 16 max
Call network
177 nodes / 137 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
14,807
Files
74
Compiled share
3.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
80
Internal functions
114
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
33.3%
Unsafe pattern score
0
Dep constraint coverage
40%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-08-21
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
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
- 21
- Examples that run
- 95%20 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 79%
- Return-value docs
- 72%
- Help pages citing references
- 29%
- No changes in this version.
From NEWS in the release
Repository practices
Checks run against github.com/bioconductor/genomicalignments on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Topics
Depended on by (150)
Show 64 packagesHide 64 packages
Bioconductor (146)
Suggested by (31)
People
- Hervé Pagès author maintainer
-
Halimat C. Atanda
contributor
Translated 'WorkingWithAlignedNucleotides' vignette from Sweave to RMarkdown / HTML.
- Fedor Bezrukov contributor
- Robert Castelo contributor
- Martin Morgan author
- Valerie Obenchain author
Cite
Cite this package
Run in R for the authors' entry:
citation("GenomicAlignments")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1371/journal.pcbi.1003118.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.