dearseq
Bioc currentDifferential Expression Analysis for RNA-seq data through a robust variance component test
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
Differential Expression Analysis RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with repeated or longitudinal data. Methods are detailed in: i) Agniel D & Hejblum BP (2017) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604 ; and ii) Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2020) dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, NAR Genomics and Bioinformatics, 2(4):lqaa093.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
19 15 exported
Complexity
9.6 avg / 61 max
Call network
19 nodes / 11 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
5,930
Files
56
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
3
Testing
Has tests
Yes
Test-to-code ratio
0.02
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
GPL-2 | file LICENSE
License flags
SPDX valid, not OSI
History
Versions
13
First release
2020-04-27
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 21 (5 internal)includes a package overview page
- Examples that run
- 100%17 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 92%
- Return-value docs
- 100%
- Help pages citing references
- 43%
- dearseqUserguide HTML
Repository practices
7 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/borishejblum/dearseq on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-10-16 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| PBT_gmt | list | 3 elements | 2 packages |
| baduel_gmt | list | 3 elements | 2 packages |
| design | data.frame | 48 × 11 | 2 packages |
| expr_norm_corr | matrix | 2,454 × 48 | 2 packages |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (3)
People
- Boris P. Hejblum author maintainer
- Denis Agniel author
- Marine Gauthier author
- Mélanie Huchon contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("dearseq")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nargab/lqaa093.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.