Rhisat2
Bioc currentR Wrapper for HISAT2 Aligner
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
2240 6 exported
Complexity
6 avg / 21 max
Call network
2240 nodes / 4743 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
153,545
Files
418
Compiled share
99.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
6
Internal functions
2
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.65
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
1 externalGNU make
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-06-11
Latest release
2026-07-29
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 9 (3 internal)includes a package overview page
- Examples that run
- 100%6 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 44%
- Rhisat2 HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/fmicompbio/rhisat2 on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| genes.granges | – | – | – |
| hisat2_splice_sites | data.frame | 25 × 4 | No other package |
| hisat2_splice_sites_diffchr | data.frame | 15 × 4 | No other package |
Topics
Depended on by (2)
Bioconductor (2)
People
- Charlotte Soneson author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("Rhisat2")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 v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.