miRspongeR
Bioc currentIdentification and analysis of miRNA sponge regulation
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
74 10 exported
Complexity
7 avg / 39 max
Call network
74 nodes / 85 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
8,017
Files
40
Compiled share
43.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
10
Internal functions
40
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
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
18
First release
2017-10-30
Latest release
2026-09-05
Avg cadence
183 days
Cold removal rate
–
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 11
- Examples that run
- 80%8 run in a plain check · 2 never run
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 64%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/zhangjunpeng411/mirsponger on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| .Random.seed | vector | 626 elements | No other package |
| ExpData | data.frame | 144 × 484 | No other package |
| Groundtruth | data.frame | 3,804 × 2 | No other package |
| MREs | data.frame | 9,621 × 5 | No other package |
| SurvData | data.frame | 144 × 3 | No other package |
| miR2Target | data.frame | 476 × 2 | No other package |
| precomputed_null_model | list | 8 elements | No other package |
Topics
People
- Junpeng Zhang author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("miRspongeR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-019-2861-y, 10.1093/bioadv/vbac063.
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.