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# 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 "cosmosR" in publications use:'
type: software
license: GPL-3.0-only
title: 'cosmosR: COSMOS (Causal Oriented Search of Multi-Omic Space)'
version: 1.13.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.cosmosR
abstract: COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates
  phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge
  of signaling, metabolic, and gene regulatory networks. It estimated the activities
  of transcrption factors and kinases and finds a network-level causal reasoning.
  Thereby, COSMOS provides mechanistic hypotheses for experimental observations across
  mulit-omics datasets.
authors:
- family-names: Dugourd
  given-names: Aurélien
  email: dugourdaurelien@gmail.com
  orcid: https://orcid.org/0000-0002-0714-028X
- family-names: Gabor
  given-names: Attila
  email: attila.gabor@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-0776-1182
- family-names: Zirngibl
  given-names: Katharina
  email: katharina.zirngibl@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-7518-0339
preferred-citation:
  type: article
  title: Causal integration of multi-omics data with prior knowledge to generate mechanistic
    hypotheses
  authors:
  - family-names: Dugourd
    given-names: Aurelien
  - family-names: Kuppe
    given-names: Christoph
  - family-names: Sciacovelli
    given-names: Marco
  - family-names: Gjerga
    given-names: Enio
  - family-names: Gabor
    given-names: Attila
    email: attila.gabor@uni-heidelberg.de
    orcid: https://orcid.org/0000-0002-0776-1182
  - family-names: Embdal
    given-names: Kristina B.
  - family-names: Vieira
    given-names: Vitor
  - family-names: Bekker-Jensen
    given-names: Dorte B.
  - family-names: Kranz
    given-names: Jennifer
  - family-names: Bindels
    given-names: Eric M. J.
  - family-names: Costa
    given-names: Ana S. H.
  - family-names: Sousa
    given-names: Abel
  - family-names: Beltrao
    given-names: Pedro
  - family-names: Olsen
    given-names: Jesper V
  - family-names: Frezza
    given-names: Christian
  - family-names: Kramann
    given-names: Rafael
  - family-names: Saez-Rodriguez
    given-names: Julio
  journal: Molecular Systems Biology
  year: '2021'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/saezlab/COSMOSR
commit: 4c05998b1b21eab5cc37b057f893b79666d782ca
url: https://github.com/saezlab/COSMOSR
contact:
- family-names: Gabor
  given-names: Attila
  email: attila.gabor@uni-heidelberg.de
  orcid: https://orcid.org/0000-0002-0776-1182