Rsubread
Bioc currentMapping, quantification and variant analysis of sequencing data
Release Lineage
Entered 2.8 · Apr 14, 2011
Current · Requires R 4.6
Description
Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
1560 0 exported
Complexity
23.5 avg / 1076 max
Call network
1560 nodes / 3123 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
81,221
Files
156
Compiled share
93.8%
Has compiled src
Yes
Language breakdown
API
Exported functions
24
Internal functions
45
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
11.1%
Unsafe pattern score
2
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL (>=3)
License flags
not SPDX, not OSI
History
Versions
31
First release
2011-07-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 22
- Examples that run
- 64%7 run in a plain check · 4 never run
- Exported functions with examples
- 50%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 77%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
Topics
Depended on by (14)
Show all 22 packagesHide all 22 packages
Bioconductor (14)
Suggested by (8)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("Rsubread")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nar/gkz114.
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.