PanomiR
Bioc currentDetection of miRNAs that regulate interacting groups of pathways
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
44 11 exported
Complexity
2.9 avg / 9 max
Call network
44 nodes / 33 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
3,275
Files
55
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
33
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
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-08-17
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 34 (10 internal)
- Examples that run
- 100%16 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- PanomiR Tutorial HTML
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/pouryany/panomir on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| gscExample | GeneSetCollection | 2 elements | 2 packages |
| miniTestsPanomiR | list | 6 elements | No other package |
| msigdb_c2 | list | 1,143 elements | No other package |
| path_gene_table | tibble | 60,715 × 3 | No other package |
| targetScan_03 | list | 439 elements | No other package |
Topics
People
- Pourya Naderi author maintainer
- Winston Hide author
- Ilya Sytchev author
- Yue Yang (Alan) Teo author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("PanomiR")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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.