strandCheckR
Bioc currentCalculate strandness information of a bam file
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 10 exported
Complexity
7.6 avg / 27 max
Call network
18 nodes / 22 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
3,408
Files
78
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
8
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.14
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
5.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2018-12-07
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Thu-Hien To author maintainer
- Stevie Pederson author
Cite
Cite this package
Start here. This is the citation for the package itself.
citation("strandCheckR")Bioconductor packages have no CRAN DOI. The package landing page is https://bioconductor.org/packages/strandCheckR.
BibTeX, derived from DESCRIPTION
@Manual{strandCheckR,
title = {strandCheckR: Calculate strandness information of a bam file},
author = {To, Thu-Hien and Pederson, Stevie},
year = {2026},
note = {R package version 1.30.0},
url = {https://bioconductor.org/packages/strandCheckR}
}Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.
This is the citation for the package. It is not a citation for the R Observatory.
Cite this page
Use this when the claim is about a measurement on this page.
BibTeX
@misc{robservatorystrandCheckR,
author = {Balamuta, James Joseph},
title = {{R} {Observatory}: Metrics for {strandCheckR} version 1.30.0},
year = {2026},
publisher = {HJJB, LLC},
url = {https://r-observatory.thecoatlessprofessor.com/bioc/strandCheckR},
note = {Data set. Data release v2026-08-05}
}APA
Balamuta, J. J. (2026). R Observatory: Metrics for strandCheckR version 1.30.0 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/bioc/strandCheckRRIS
TY - DATA
AU - Balamuta, James Joseph
TI - R Observatory: Metrics for strandCheckR version 1.30.0
PY - 2026
PB - HJJB, LLC
N1 - Data release v2026-08-05
UR - https://r-observatory.thecoatlessprofessor.com/bioc/strandCheckR
ER - In prose
These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/bioc/strandCheckR.Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.