To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MoonlightR")

In most cases, you don't need to download the package archive at all.

MoonlightR

 

Identify oncogenes and tumor suppressor genes from omics data

Bioconductor version: Release (3.5)

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*, Catharina Olsen*, Claudia Cava, Thilde Terkelsen, Laura Cantini, Andre Olsen, Gloria Bertoli, Andrei Zinovyev, Emmanuel Barillot, Isabella Castiglioni, Elena Papaleo, Gianluca Bontempi

Maintainer: Antonio Colaprico <antonio.colaprico at ulb.ac.be>, Catharina Olsen <colsen at ulb.ac.be>

Citation (from within R, enter citation("MoonlightR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MoonlightR")

Documentation

HTML R Script Vignette Title
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, GeneSetEnrichment, MethylationArray, Network, NetworkEnrichment, Pathways, Software, Survival
Version 1.2.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License GPL (>= 3)
Depends R (>= 3.3), doParallel, foreach
Imports parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png
SystemRequirements
Enhances
URL https://github.com/torongs82/Moonlight
BugReports https://github.com/torongs82/Moonlight/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source MoonlightR_1.2.0.tar.gz
Windows Binary MoonlightR_1.2.0.zip
Mac OS X 10.11 (El Capitan) MoonlightR_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/MoonlightR/tree/release-3.5
Package Short Url http://bioconductor.org/packages/MoonlightR/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: