MoonlightR
This is the development version of MoonlightR; for the stable release version, see MoonlightR.
Identify oncogenes and tumor suppressor genes from omics data
Bioconductor version: Development (3.18)
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.
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]
Maintainer: Matteo Tiberti <tiberti at cancer.dk>
citation("MoonlightR")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("MoonlightR")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MoonlightR")| Vignette Title | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, GeneSetEnrichment, MethylationArray, Network, NetworkEnrichment, Pathways, Software, Survival |
| Version | 1.27.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7 years) |
| License | GPL (>= 3) |
| 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 |
| Linking To | |
| Suggests | BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR |
| System Requirements | |
| Enhances | |
| URL | https://github.com/ELELAB/MoonlightR |
| Bug Reports | https://github.com/ELELAB/MoonlightR/issues |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MoonlightR_1.27.1.tar.gz |
| Windows Binary | MoonlightR_1.27.1.zip (64-bit only) |
| macOS Binary (x86_64) | MoonlightR_1.27.1.tgz |
| macOS Binary (arm64) | MoonlightR_1.27.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MoonlightR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MoonlightR |
| Bioc Package Browser | https://code.bioconductor.org/browse/MoonlightR/ |
| Package Short Url | https://bioconductor.org/packages/MoonlightR/ |
| Package Downloads Report | Download Stats |