MoonlightR
Bioc currentIdentify oncogenes and tumor suppressor genes from omics data
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
14 14 exported
Complexity
7.4 avg / 32 max
Call network
14 nodes / 6 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
3,155
Files
71
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
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
3.5
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
189 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
- 27includes a package overview page
- Examples that run
- 86%12 run in a plain check · 2 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Vignette Title HTML
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/elelab/moonlightr on 2026-10-22.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DEGsmatrix | data.frame | 3,390 × 5 | 2 packages |
| DiseaseList | list | 101 elements | No other package |
| EAGenes | data.frame | 20,038 × 5 | 3 packages |
| GDCprojects | vector | 39 elements | No other package |
| GEO_TCGAtab | data.frame | 18 × 12 | 2 packages |
| dataFilt | matrix | 13,742 × 20 | No other package |
| dataGRN | list | 2 elements | No other package |
| dataURA | matrix | 100 × 2 | No other package |
| geneInfo | matrix | 20,531 × 3 | 2 packages |
| knownDriverGenes | list | 2 elements | 2 packages |
| listMoonlight | list | 5 elements | 2 packages |
| tabGrowBlock | data.frame | 101 × 3 | 2 packages |
Topics
People
- Matteo Tiberti maintainer author
- Matthew H. Bailey author
- Emmanuel Barillot author
- Gloria Bertoli author
- Gianluca Bontempi author
- Laura Cantini author
- Isabella Castiglioni author
- Claudia Cava author
- Xi Steven Chen author
- Antonio Colaprico author
- Mona Nourbakhsh author
- Houtan Noushmehr author
- Gabriel J. Odom author
- André V. Olsen author
- Catharina Olsen author
- Elena Papaleo author
- Astrid Saksager author
- Tiago C. Silva author
- Thilde Terkelsen author
- Andrei Zinovyev author
Cite
Cite this package
Run in R for the authors' entry:
citation("MoonlightR")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.