cleanUpdTSeq
Bioc currentcleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
Release Lineage
Entered 2.13 · Oct 15, 2013
Current · Requires R 4.6
Description
This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
5 5 exported
Complexity
11.8 avg / 22 max
Call network
5 nodes / 1 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
1,386
Files
33
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
0
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
–
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
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
26
First release
2013-11-22
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12includes a package overview page
- Examples that run
- 100%8 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 8%
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
| Name | Class | Size | Also in |
|---|---|---|---|
| Ndata.NaiveBayes | data.frame | 9,219 × 74 | No other package |
| Pdata.NaiveBayes | data.frame | 22,770 × 74 | No other package |
| classifier | – | – | – |
| data.NaiveBayes | list | 2 elements | No other package |
| test-predNaiveBayes | data.frame | 27 × 6 | No other package |
| testSet.NaiveBayes | – | – | – |
Topics
Depended on by (1)
Bioconductor (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("cleanUpdTSeq")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btt446.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.