InPAS
Bioc currentIdentify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
67 34 exported
Complexity
8.4 avg / 42 max
Call network
67 nodes / 99 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
11,335
Files
131
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
34
Internal functions
33
Testing
Has tests
Yes
Test-to-code ratio
0.00
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
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
23
First release
2015-07-28
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
27
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 67 (31 internal)includes a package overview page
- Examples that run
- 90%19 run in a plain check (7 of them under a condition) · 2 never run
- Exported functions with examples
- 47%
- Documented parameters
- 99%
- Return-value docs
- 68%
- Help pages citing references
- 3%
- InPAS Vignette HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
Topics
People
- Jianhong Ou author maintainer
- Michael R. Green author
- Haibo Liu author
- Sungmi M. Park author
- Lihua Julie Zhu author
Cite
Cite this package
Run in R for the authors' entry:
citation("InPAS")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.31083/j.fbs1604021.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.