# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "decoupleR" in publications use:'
type: software
license: GPL-3.0-only
title: 'decoupleR: decoupleR: Ensemble of computational methods to infer biological
  activities from omics data'
version: 2.11.0
doi: 10.1093/bioadv/vbac016
abstract: Many methods allow us to extract biological activities from omics data using
  information from prior knowledge resources, reducing the dimensionality for increased
  statistical power and better interpretability. Here, we present decoupleR, a Bioconductor
  package containing different statistical methods to extract these signatures within
  a unified framework. decoupleR allows the user to flexibly test any method with
  any resource. It incorporates methods that take into account the sign and weight
  of network interactions. decoupleR can be used with any omic, as long as its features
  can be linked to a biological process based on prior knowledge. For example, in
  transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics
  phosphosites that are targeted by a kinase.
authors:
- family-names: Badia-i-Mompel
  given-names: Pau
  email: pau.badia@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-1004-3923
- family-names: Vélez-Santiago
  given-names: Jesús
  email: jvelezmagic@gmail.com
  orcid: https://orcid.org/0000-0001-5128-3838
- family-names: Braunger
  given-names: Jana
  email: jana.bc@gmx.de
  orcid: https://orcid.org/0000-0003-0820-9987
- family-names: Geiss
  given-names: Celina
  email: celina.geiss@stud.uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-8740-706X
- family-names: Dimitrov
  given-names: Daniel
  email: daniel.dimitrov@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-5197-2112
- family-names: Müller-Dott
  given-names: Sophia
  email: sophia.mueller-dott@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-9710-1865
- family-names: Taus
  given-names: Petr
  email: petr.taus@ceitec.muni.cz
  orcid: https://orcid.org/0000-0003-3764-9033
- family-names: Dugourd
  given-names: Aurélien
  email: aurelien.dugourd@bioquant.uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-0714-028X
- family-names: Holland
  given-names: Christian H.
  email: cholland2408@gmail.com
  orcid: https://orcid.org/0000-0002-3060-5786
- family-names: Ramirez Flores
  given-names: Ricardo O.
  email: roramirezf@uni-heidelberg.de
  orcid: https://orcid.org/0000-0003-0087-371X
- family-names: Saez-Rodriguez
  given-names: Julio
  email: pub.saez@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-8552-8976
preferred-citation:
  type: article
  title: 'decoupleR: ensemble of computational methods to infer biological activities
    from omics data'
  authors:
  - family-names: Badia-i-Mompel
    given-names: Pau
    email: pau.badia@uni-heidelberg.de
    orcid: https://orcid.org/0000-0002-1004-3923
  - family-names: Santiago
    given-names: Jesús Vélez
  - family-names: Braunger
    given-names: Jana
    email: jana.bc@gmx.de
    orcid: https://orcid.org/0000-0003-0820-9987
  - family-names: Geiss
    given-names: Celina
    email: celina.geiss@stud.uni-heidelberg.de
    orcid: https://orcid.org/0000-0002-8740-706X
  - family-names: Dimitrov
    given-names: Daniel
    email: daniel.dimitrov@uni-heidelberg.de
    orcid: https://orcid.org/0000-0002-5197-2112
  - family-names: Müller-Dott
    given-names: Sophia
    email: sophia.mueller-dott@uni-heidelberg.de
    orcid: https://orcid.org/0000-0002-9710-1865
  - family-names: Taus
    given-names: Petr
    email: petr.taus@ceitec.muni.cz
    orcid: https://orcid.org/0000-0003-3764-9033
  - family-names: Dugourd
    given-names: Aurelien
  - family-names: Holland
    given-names: Christian H.
    email: cholland2408@gmail.com
    orcid: https://orcid.org/0000-0002-3060-5786
  - family-names: Flores
    given-names: Ricardo O. Ramirez
  - family-names: Saez-Rodriguez
    given-names: Julio
    email: pub.saez@uni-heidelberg.de
    orcid: https://orcid.org/0000-0002-8552-8976
  journal: Bioinformatics Advances
  year: '2022'
  doi: 10.1093/bioadv/vbac016
repository: https://bioc.r-universe.dev
repository-code: https://github.com/saezlab/decoupleR
url: https://saezlab.github.io/decoupleR/
contact:
- family-names: Badia-i-Mompel
  given-names: Pau
  email: pau.badia@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-1004-3923