EDASeq
Bioc currentExploratory Data Analysis and Normalization for RNA-Seq
Release Lineage
Entered 2.9 · Nov 1, 2011
Current · Requires R 4.6
Description
Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
10 2 exported
Complexity
4.5 avg / 12 max
Call network
10 nodes / 6 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
2,732
Files
39
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
8
Testing
Has tests
Yes
Test-to-code ratio
0.13
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
28.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
30
First release
2011-10-31
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
–
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 19includes a package overview page
- Examples that run
- 90%9 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 67%
- Documented parameters
- 73%
- Return-value docs
- 67%
- Help pages citing references
- 16%
- EDASeq Vignette HTML
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/drisso/edaseq on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| yeastGC | vector | 6,717 elements | No other package |
| yeastLength | vector | 6,717 elements | No other package |
Topics
Depended on by (7)
Show all 15 packagesHide all 15 packages
Bioconductor (7)
Suggested by (8)
People
- Davide Risso author maintainer copyright holder
- Sandrine Dudoit author
- Ludwig Geistlinger contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("EDASeq")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.