CleanUpRNAseq
Bioc currentDetect and Correct Genomic DNA Contamination in RNA-seq Data
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
23 18 exported
Complexity
5.3 avg / 17 max
Call network
23 nodes / 5 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
6,213
Files
52
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
19
Internal functions
5
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 24 (1 internal)includes a package overview page
- Examples that run
- 100%18 run in a plain check (6 of them under a condition)
- Exported functions with examples
- 95%
- Documented parameters
- 94%
- Return-value docs
- 95%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/haibol2016/cleanuprnaseq on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| example.colData | data.frame | 8 × 6 | No other package |
| feature_counts_list | list | 7 elements | No other package |
| gene_GC | data.frame | 62,754 × 2 | No other package |
| intergenic_GC | data.frame | 2,000 × 2 | No other package |
| salmon_quant | list | 3 elements | No other package |
Topics
People
- Haibo Liu author maintainer
- Kai Hu author
- Michelle Kelliher contributor
- Kevin O'Connor contributor
- Lihua Julie Zhu author
Cite
Cite this package
Run in R for the authors' entry:
citation("CleanUpRNAseq")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.3390/biotech13030030.
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.