MoonlightR
Identify oncogenes and tumor suppressor genes from omics data
Bioconductor version: 3.24 · Package version: 1.39.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MoonlightR")Details
| Maintainer | Matteo Tiberti <tiberti@cancer.dk> |
| Author | Antonio Colaprico [aut], Catharina Olsen [aut], Matthew H. Bailey [aut], Gabriel J. Odom [aut], Thilde Terkelsen [aut], Mona Nourbakhsh [aut], Astrid Saksager [aut], Tiago C. Silva [aut], André V. Olsen [aut], Laura Cantini [aut], Andrei Zinovyev [aut], Emmanuel Barillot [aut], Houtan Noushmehr [aut], Gloria Bertoli [aut], Isabella Castiglioni [aut], Claudia Cava [aut], Gianluca Bontempi [aut], Xi Steven Chen [aut], Elena Papaleo [aut], Matteo Tiberti [cre, aut] |
| License | GPL (>= 3) |
| URL | https://github.com/ELELAB/MoonlightR |
| Bug Reports | https://github.com/ELELAB/MoonlightR/issues |
| Status | Deprecated |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, GeneSetEnrichment, MethylationArray, Network, NetworkEnrichment, Pathways, Software, Survival |
| Package Short Url | https://bioconductor.org/packages/MoonlightR/ |
Citation
From within R, enter citation("MoonlightR"):
Antonio Colaprico, Catharina Olsen, Matthew H. Bailey, Gabriel J. Odom, Thilde Terkelsen, Mona Nourbakhsh, Astrid Saksager, Tiago C. Silva, André V. Olsen, Laura Cantini, Andrei Zinovyev, Emmanuel Barillot, Houtan Noushmehr, Gloria Bertoli, Isabella Castiglioni, Claudia Cava, Gianluca Bontempi, Xi Steven Chen, Elena Papaleo, Matteo Tiberti. MoonlightR: Identify oncogenes and tumor suppressor genes from omics data. doi:10.18129/B9.bioc.MoonlightR, R package version 1.39.1, https://bioconductor.org/packages/MoonlightR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | MoonlightR_1.39.1.tar.gz |
| Windows binary (x86_64) | MoonlightR_1.39.1.zip |
| macOS binary (arm64) | MoonlightR_1.39.1.tgz |
| macOS binary (x86_64) | MoonlightR_1.39.1.tgz |
Dependencies
Depends: R (>= 3.5), doParallel, foreach
Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils
Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR