DEXSeq
Bioc currentInference of differential exon usage in RNA-Seq
Release Lineage
Entered 2.9 · Nov 1, 2011
Current · Requires R 4.6
Description
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
47 16 exported
Complexity
4.6 avg / 38 max
Call network
47 nodes / 44 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
3,836
Files
37
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
27
Testing
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
Docs
Roxygen coverage
80%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
23.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
30
First release
2011-12-06
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
14
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 17
- Examples that run
- 62%8 run in a plain check · 5 never run
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 78%
- Help pages citing references
- 6%
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.
Topics
Depended on by (7)
Show all 14 packagesHide all 14 packages
Bioconductor (7)
Suggested by (7)
People
- Hugo Gruson maintainer
- Simon Anders author
-
Alejandro Reyes
author
ccp
Maintainer until 2026.
Cite
Cite this package
Run in R for the authors' entry:
citation("DEXSeq")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/gr.133744.111, 10.1073/pnas.1307202110.
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.