APAlyzer
Bioc currentA toolkit for APA analysis using RNA-seq data
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
60 12 exported
Complexity
2.3 avg / 10 max
Call network
60 nodes / 55 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
2,648
Files
42
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
12
Internal functions
47
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
LGPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2019-10-29
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
17
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- 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/rjwangbioinfo/apalyzer on 2026-10-11.
GitHub Pages site last deployed 2026-04-05
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DFUTRraw | data.frame | 430 × 31 | No other package |
| IPA_OUTraw | data.frame | 536 × 45 | No other package |
| dfIPA | data.frame | 16,893 × 7 | No other package |
| dfLE | data.frame | 6,882 × 5 | No other package |
| refUTRraw | data.frame | 11,735 × 6 | No other package |
| test_3UTRAPA | data.frame | 1,289 × 5 | No other package |
| test_3UTRmuti | data.frame | 258 × 4 | No other package |
| test_3UTRsing | data.frame | 285 × 4 | No other package |
| test_IPA | data.frame | 1,361 × 6 | No other package |
| test_IPAmuti | data.frame | 226 × 5 | No other package |
| test_IPAsing | data.frame | 202 × 5 | No other package |
Topics
People
- Ruijia Wang maintainer author
- Wei-Chun Chen author
- Bin Tian author
Cite
Cite this package
Run in R for the authors' entry:
citation("APAlyzer")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btaa266.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.