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# CITATION.cff 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 "hcocena" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'hcocena: Horizontal Integration and Analysis of Multiple Transcriptomics Datasets'
version: 0.99.12
doi: 10.1093/bioinformatics/btac589
identifiers:
- type: doi
  value: 10.32614/CRAN.package.hcocena
abstract: Tools for the joint analysis of multiple transcriptomics datasets using
  a network-based integration approach. The package provides an S4 object model based
  on MultiAssayExperiment for reproducible analysis of single-layer and multi-layer
  studies. It includes workflows for clustering, module visualization, functional
  annotation, upstream inference, and longitudinal follow-up while retaining compatibility
  helpers for legacy hCoCena objects.
authors:
- family-names: Ulas
  given-names: Thomas
  email: t.ulas@uni-bonn.de
  orcid: https://orcid.org/0000-0002-9785-4197
preferred-citation:
  type: article
  title: 'hCoCena: horizontal integration and analysis of transcriptomics datasets'
  authors:
  - family-names: Oestreich
    given-names: Marie
  - family-names: Holsten
    given-names: Lisa
  - family-names: Agrawal
    given-names: Shobhit
  - family-names: Dahm
    given-names: Kilian
  - family-names: Koch
    given-names: Philipp
  - family-names: Jin
    given-names: Han
  - family-names: Becker
    given-names: Matthias
  - family-names: Ulas
    given-names: Thomas
    email: t.ulas@uni-bonn.de
    orcid: https://orcid.org/0000-0002-9785-4197
  journal: Bioinformatics
  year: '2022'
  volume: '38'
  issue: '20'
  doi: 10.1093/bioinformatics/btac589
  start: 4727-4734
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/BioCompNet/hcocena
commit: d0b918c0e0b390678cceba94ccaa9d2fc0ddd95d
url: https://github.com/BioCompNet/hcocena
date-released: '2026-10-03'
contact:
- family-names: Ulas
  given-names: Thomas
  email: t.ulas@uni-bonn.de
  orcid: https://orcid.org/0000-0002-9785-4197
references:
- type: article
  title: 'hCoCena: A toolbox for network-based co-expression analysis and horizontal
    integration of transcriptomic datasets'
  authors:
  - family-names: Holsten
    given-names: Lisa
  - family-names: Dahm
    given-names: Kilian
  - family-names: Oestreich
    given-names: Marie
  - family-names: Becker
    given-names: Matthias
  - family-names: Ulas
    given-names: Thomas
  journal: STAR Protocols
  year: '2024'
  volume: '5'
  issue: '1'
  doi: 10.1016/j.xpro.2024.102922
  start: '102922'