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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 "netZooR" in publications use:'
type: software
license: GPL-3.0-only
title: 'netZooR: Unified methods for the inference and analysis of gene regulatory
  networks'
version: 1.9.0
doi: 10.1186/s13059-023-02877-1 7
abstract: netZooR unifies the implementations of several Network Zoo methods (netzoo,
  netzoo.github.io) into a single package by creating interfaces between network inference
  and network analysis methods. Currently, the package has 3 methods for network inference
  including PANDA and its optimized implementation OTTER (network reconstruction using
  mutliple lines of biological evidence), LIONESS (single-sample network inference),
  and EGRET (genotype-specific networks). Network analysis methods include CONDOR
  (community detection), ALPACA (differential community detection), CRANE (significance
  estimation of differential modules), MONSTER (estimation of network transition states).
  In addition, YARN allows to process gene expresssion data for tissue-specific analyses
  and SAMBAR infers missing mutation data based on pathway information.
authors:
- family-names: Ben Guebila
  given-names: Marouen
  email: benguebila@hsph.harvard.edu
  orcid: https://orcid.org/0000-0001-5934-966X
- family-names: Wang
  given-names: Tian
  email: tian.wang@bc.edu
  orcid: https://orcid.org/0000-0002-2767-3243
- family-names: Platig
  given-names: John
  email: john.platig@channing.harvard.edu
- family-names: Kuijjer
  given-names: Marieke
  email: marieke.kuijjer@ncmm.uio.no
  orcid: https://orcid.org/0000-0001-6280-3130
- family-names: Padi
  given-names: Megha
  email: mpadi@email.arizona.edu
  orcid: https://orcid.org/0000-0002-3446-4562
- family-names: Burkholz
  given-names: Rebekka
  email: rburkholz@hsph.harvard.edu
- family-names: Weighill
  given-names: Des
  orcid: https://orcid.org/0000-0003-4979-5871
- family-names: Shutta
  given-names: Kate
  orcid: https://orcid.org/0000-0003-0402-3771
preferred-citation:
  type: article
  title: 'The Network Zoo: a multilingual package for the inference and analysis of
    biological networks'
  authors:
  - family-names: Guebila
    given-names: Marouen Ben
  - family-names: Wang
    given-names: Tian
    email: tian.wang@bc.edu
    orcid: https://orcid.org/0000-0002-2767-3243
  - family-names: Lopes-Ramos
    given-names: Camila M
  - family-names: Fanfani
    given-names: Viola
  - family-names: Quackenbush
    given-names: John
  year: '2023'
  journal: Genome Biology
  doi: 10.1186/s13059-023-02877-1 7
repository: https://bioc.r-universe.dev
repository-code: https://github.com/netZoo/netZooR
url: https://netzoo.github.io/
date-released: '2023-03-27'
contact:
- family-names: Ben Guebila
  given-names: Marouen
  email: benguebila@hsph.harvard.edu
  orcid: https://orcid.org/0000-0001-5934-966X