CAGEfightR
Bioc currentAnalysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
68 34 exported
Complexity
1.8 avg / 7 max
Call network
68 nodes / 20 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
9,839
Files
98
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
57
Internal functions
34
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
100%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
17
First release
2018-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
10
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 55
- Examples that run
- 76%42 run in a plain check · 8 never run · 5 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/maltethodberg/cagefightr on 2026-10-25.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| exampleBidirectional | – | – | – |
| exampleCTSSs | – | – | – |
| exampleDesign | – | – | – |
| exampleGenes | – | – | – |
| exampleUnidirectional | – | – | – |
Topics
Depended on by (2)
Bioconductor (2)
Suggested by (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("CAGEfightR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-019-3029-5.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.