DESeq2
Bioc currentDifferential gene expression analysis based on the negative binomial distribution
Release Lineage
Entered 2.12 · Apr 4, 2013
Current · Requires R 4.6
Description
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
133 34 exported
Complexity
6.8 avg / 68 max
Call network
133 nodes / 214 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
17,052
Files
105
Compiled share
3.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
44
Internal functions
89
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
0
Dep constraint coverage
35.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
LGPL (>= 3)
License flags
not SPDX, not OSI
History
Versions
27
First release
2013-08-14
Latest release
2026-04-28
Avg cadence
177 days
Cold removal rate
100%
Dep drift
18
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 40includes a package overview page
- Examples that run
- 100%29 run in a plain check
- Exported functions with examples
- 71%
- Documented parameters
- 99%
- Return-value docs
- 71%
- Help pages citing references
- 23%
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/thelovelab/deseq2 on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| pasilla_gene_counts | data.frame | 14,599 × 8 | 2 packages |
| pasilla_sample_annotation | data.frame | 7 × 6 | 2 packages |
Topics
Depended on by (147)
Show 77 packagesHide 77 packages
Bioconductor (130)
CRAN (17)
Suggested by (114)
People
- Michael Love author maintainer
- CZI funder
- NIH NHGRI funder
- RADIANT EU FP7 funder
- Constantin Ahlmann-Eltze contributor
- Simon Anders author contributor
- Kwame Forbes contributor
- Wolfgang Huber author contributor
- Nikolaos Ignatiadis contributor
- Raphael Rossellini contributor
- Anqi Zhu contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("DESeq2")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-014-0550-8.
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.