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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "MoonlightR" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'MoonlightR: Identify oncogenes and tumor suppressor genes from omics data'
version: 1.31.0
abstract: '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.'
authors:
- family-names: Colaprico
  given-names: Antonio
- family-names: Olsen
  given-names: Catharina
- family-names: Bailey
  given-names: Matthew H.
- family-names: Odom
  given-names: Gabriel J.
- family-names: Terkelsen
  given-names: Thilde
- family-names: Nourbakhsh
  given-names: Mona
- family-names: Saksager
  given-names: Astrid
- family-names: Silva
  given-names: Tiago C.
- family-names: Olsen
  given-names: André V.
- family-names: Cantini
  given-names: Laura
- family-names: Zinovyev
  given-names: Andrei
- family-names: Barillot
  given-names: Emmanuel
- family-names: Noushmehr
  given-names: Houtan
- family-names: Bertoli
  given-names: Gloria
- family-names: Castiglioni
  given-names: Isabella
- family-names: Cava
  given-names: Claudia
- family-names: Bontempi
  given-names: Gianluca
- family-names: Chen
  given-names: Xi Steven
- family-names: Papaleo
  given-names: Elena
- family-names: Tiberti
  given-names: Matteo
  email: tiberti@cancer.dk
preferred-citation:
  type: article
  title: Interpreting pathways to discover cancer driver genes with Moonlight
  authors:
  - family-names: Colaprico
    given-names: Antonio
  - family-names: Olsen
    given-names: Catharina
  - family-names: Bailey
    given-names: Matthew H.
  - family-names: Odom
    given-names: Gabriel J.
  - family-names: Terkelsen
    given-names: Thilde
  - family-names: Silva
    given-names: Tiago C.
  - family-names: Olsen
    given-names: André V.
  - family-names: Cantini
    given-names: Laura
  - family-names: Zinovyev
    given-names: Andrei
  - family-names: Barillot
    given-names: Emmanuel
  - family-names: Noushmehr
    given-names: Houtan
  - family-names: Bertoli
    given-names: Gloria
  - family-names: Castiglioni
    given-names: Isabella
  - family-names: Cava
    given-names: Claudia
  - family-names: Bontempi
    given-names: Gianluca
  - family-names: Chen
    given-names: Xi Steven
  - family-names: Papaleo
    given-names: Elena
  journal: Nature Communications
  year: '2020'
  volume: 11(69)
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ELELAB/MoonlightR
url: https://github.com/ELELAB/MoonlightR
date-released: 7-08-20
contact:
- family-names: Tiberti
  given-names: Matteo
  email: tiberti@cancer.dk