CAGEr
Bioc currentAnalysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Release Lineage
Entered 2.12 · Apr 4, 2013
Current · Requires R 4.6
Description
The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
80 3 exported
Complexity
3.4 avg / 62 max
Call network
80 nodes / 52 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
16,047
Files
182
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
72
Internal functions
77
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
66.7%
Unsafe pattern score
0
Dep constraint coverage
27.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
27
First release
2013-09-02
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
34
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 97%
- Documented parameters
- 91%
- Return-value docs
- 81%
- References docs
- 11%
Topics
Depended on by (2)
Bioconductor (2)
People
- Charles Plessy maintainer
- Damir Baranasic contributor
- Katalin Ferenc contributor
- Vanja Haberle author
- Sarvesh Nikumbh contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("CAGEr")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.