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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 "COTAN" in publications use:'
type: software
license: GPL-3.0-only
title: 'COTAN: COexpression Tables ANalysis'
version: 2.5.6
abstract: Statistical and computational method to analyze the co-expression of gene
  pairs at single cell level. It provides the foundation for single-cell gene interactome
  analysis. The basic idea is studying the zero UMI counts' distribution instead of
  focusing on positive counts; this is done with a generalized contingency tables
  framework. COTAN can effectively assess the correlated or anti-correlated expression
  of gene pairs. It provides a numerical index related to the correlation and an approximate
  p-value for the associated independence test. COTAN can also evaluate whether single
  genes are differentially expressed, scoring them with a newly defined global differentiation
  index. Moreover, this approach provides ways to plot and cluster genes according
  to their co-expression pattern with other genes, effectively helping the study of
  gene interactions and becoming a new tool to identify cell-identity marker genes.
authors:
- family-names: Silvia Giulia
  given-names: Galfrè
  email: silvia.galfre@di.unipi.it
  orcid: https://orcid.org/0000-0002-2770-0344
- family-names: Francesco
  given-names: Morandin
  email: francesco.morandin@unipr.it
  orcid: https://orcid.org/0000-0002-2022-2300
- family-names: Marco
  given-names: Fantozzi
  email: marco.fantozzi@gmail.com
  orcid: https://orcid.org/0000-0002-0708-5495
- family-names: Marco
  given-names: Pietrosanto
  orcid: https://orcid.org/0000-0001-5129-6065
- family-names: Daniel
  given-names: Puttini
  orcid: https://orcid.org/0009-0006-8401-9949
- family-names: Corrado
  given-names: Priami
  orcid: https://orcid.org/0000-0002-3261-6235
- family-names: Federico
  given-names: Cremisi
  orcid: https://orcid.org/0000-0003-4925-2703
- family-names: Manuela
  given-names: Helmer-Citterich
  orcid: https://orcid.org/0000-0001-9530-7504
repository: https://bioc.r-universe.dev
repository-code: https://github.com/seriph78/COTAN
url: https://github.com/seriph78/COTAN
contact:
- family-names: Silvia Giulia
  given-names: Galfrè
  email: silvia.galfre@di.unipi.it
  orcid: https://orcid.org/0000-0002-2770-0344