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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 "csdR" in publications use:'
type: software
license: GPL-3.0-only
title: 'csdR: Differential gene co-expression'
version: 1.11.0
doi: 10.1186/s12859-022-04605-1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.csdR
abstract: This package contains functionality to run differential gene co-expression
  across two different conditions. The algorithm is inspired by Voigt et al. 2017
  and finds Conserved, Specific and Differentiated genes (hence the name CSD). This
  package include efficient and variance calculation by bootstrapping and Welford's
  algorithm.
authors:
- family-names: Pettersen
  given-names: Jakob Peder
  email: jakobpeder.pettersen@gmail.com
  orcid: https://orcid.org/0000-0002-3485-1634
preferred-citation:
  type: article
  title: csdR, an R package for differential co-expression analysis
  authors:
  - family-names: Pettersen
    given-names: Jakob P
  - family-names: Almaas
    given-names: Eivind
  journal: BMC Bioinformatics
  year: '2022'
  month: '2'
  volume: '23'
  issue: '1'
  abstract: Differential co-expression network analysis has become an important tool
    to gain understanding of biological phenotypes and diseases. The CSD algorithm
    is a method to generate differential co-expression networks by comparing gene
    co-expressions from two different conditions. Each of the gene pairs is assigned
    conserved (C), specific (S) and differentiated (D) scores based on the co-expression
    of the gene pair between the two conditions. The result of the procedure is a
    network where the nodes are genes and the links are the gene pairs with the highest
    C-, S-, and D-scores. However, the existing CSD-implementations suffer from poor
    computational performance, difficult user procedures and lack of documentation.
  issn: 1471-2105
  doi: 10.1186/s12859-022-04605-1
  url: https://doi.org/10.1186/s12859-022-04605-1
  start: '79'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/AlmaasLab/csdR
commit: 14407273b7752f26d52e3cc78db6603f3e7ca680
url: https://almaaslab.github.io/csdR
date-released: 4-02-20
contact:
- family-names: Pettersen
  given-names: Jakob Peder
  email: jakobpeder.pettersen@gmail.com
  orcid: https://orcid.org/0000-0002-3485-1634