scanMiR
Bioc currentscanMiR
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
38 16 exported
Complexity
8.1 avg / 53 max
Call network
38 nodes / 44 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
3,324
Files
46
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
16
Internal functions
22
Testing
Has tests
Yes
Test-to-code ratio
0.15
testthat edition
3
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
4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 20
- Examples that run
- 100%19 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- 2_Kdmodels HTML
- 1_scanning HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
2 practices detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| SampleKdModel | KdModel | 10 elements | No other package |
| SampleTranscript | vector | 1 element | No other package |
Topics
Depended on by (2)
Bioconductor (2)
People
- Pierre-Luc Germain maintainer author
- Fridolin Gross author
- Michael Soutschek author
Cite
Cite this package
Run in R for the authors' entry:
citation("scanMiR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btac110.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.