Rbowtie
Bioc currentR bowtie wrapper
Release Lineage
Entered 2.9 · Nov 1, 2011
Current · Requires R 4.6
Description
This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
1077 0 exported
Complexity
12.9 avg / 40 max
Call network
1077 nodes / 2168 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
62,379
Files
153
Compiled share
97.8%
Has compiled src
Yes
Language breakdown
API
Exported functions
6
Internal functions
3
Testing
Has tests
Yes
Test-to-code ratio
0.66
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
1 externalGNU make
C++ standard
–
License
Artistic-2.0 | file LICENSE
License flags
SPDX valid, not OSI
History
Versions
30
First release
2011-10-31
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 3includes a package overview page
- Examples that run
- 100%2 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 100%
Repository practices
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/fmicompbio/rbowtie on 2026-10-25.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2023-01-29 · The repository has a site deploy workflow
Topics
Depended on by (5)
Bioconductor (5)
Suggested by (2)
People
- Michael Stadler author maintainer
- Florian Hahne author
- Anita Lerch author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("Rbowtie")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.