derfinder
Bioc currentAnnotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 26 exported
Complexity
7.4 avg / 31 max
Call network
49 nodes / 83 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
11,583
Files
156
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
26
Internal functions
23
Testing
Has tests
Yes
Test-to-code ratio
0.15
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
15
Dep constraint coverage
60%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
24
First release
2014-11-24
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 33 (1 internal)includes a package overview page
- Examples that run
- 100%26 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 97%
- Return-value docs
- 100%
- Help pages citing references
- 15%
Repository practices
13 development-tooling and community-health practices detected across 5 families in the upstream repository
Checks run against github.com/lcolladotor/derfinder on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
The repository owner accepts GitHub Sponsors
GitHub Pages site last deployed 2026-03-31 · The repository has a site deploy workflow
Show all practicesHide 1 practice
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| annotation | data.frame | 33 × 15 | No other package |
| fstats | – | – | – |
| genomeData | list | 2 elements | No other package |
| genomeDataRaw | list | 2 elements | No other package |
| genomeFstats | – | – | – |
| genomeInfo | data.frame | 31 × 5 | No other package |
| genomeRegions | list | 4 elements | No other package |
| genomicState | – | – | – |
| optionsStats | list | 14 elements | No other package |
| prep | list | 5 elements | No other package |
| regions | list | 4 elements | No other package |
| timeinfo | POSIXct | 11 elements | No other package |
Topics
Depended on by (7)
Bioconductor (7)
Suggested by (1)
People
- Leonardo Collado-Torres author maintainer
- Alyssa C. Frazee contributor
- Andrew E. Jaffe author
- Jeffrey T. Leek author thesis advisor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("derfinder")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
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.